Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond.

PubMed

Lu, Norman; Chung, Wei-Cheng; Ley, Rebecca M; Lin, Kwan-Yu; Francisco, Joseph S; Negishi, Ei-Ichi

2016-03-03

Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.

Combined Molecular Dynamics, Atoms in Molecules, and IR Studies of the Bulk Monofluoroethanol and Bulk Ethanol To Understand the Role of Organic Fluorine in the Hydrogen Bond Network.

PubMed

Biswas, Biswajit; Mondal, Saptarsi; Singh, Prashant Chandra

2017-02-16

The presence of the fluorocarbon group in fluorinated alcohols makes them an important class of molecules that have diverse applications in the field of separation techniques, synthetic chemistry, polymer industry, and biology. In this paper, we have performed the density function theory calculation along with atom in molecule analysis, molecular dynamics simulation, and IR measurements of bulk monofluoroethanol (MFE) and compared them with the data for bulk ethanol (ETH) to understand the effect of the fluorocarbon group in the structure and the hydrogen bond network of bulk MFE. It has been found that the intramolecular O-H···F hydrogen bond is almost absent in bulk MFE. Molecular dynamics simulation and density function theory calculation along with atom in molecule analysis clearly depict that in the case of bulk MFE, a significant amount of intermolecular O-H···F and C-H···F hydrogen bonds are present along with the intermolecular O-H···O hydrogen bond. The presence of intermolecular O-H···F and C-H···F hydrogen bonds causes the difference in the IR spectrum of bulk MFE as compared to bulk ETH. This study clearly depicts that the organic fluorine (fluorocarbon) of MFE acts as a hydrogen bond acceptor and plays a significant role in the structure and hydrogen bond network of bulk MFE through the formation of weak O-H···F as well C-H···F hydrogen bonds, which may be one of the important reasons behind the unique behavior of the fluoroethanols.

Hydrogen release at metal-oxide interfaces: A first principle study of hydrogenated Al/SiO2 interfaces

NASA Astrophysics Data System (ADS)

Huang, Jianqiu; Tea, Eric; Li, Guanchen; Hin, Celine

2017-06-01

The Anode Hydrogen Release (AHR) mechanism at interfaces is responsible for the generation of defects, that traps charge carriers and can induce dielectric breakdown in Metal-Oxide-Semiconductor Field Effect Transistors. The AHR has been extensively studied at Si/SiO2 interfaces but its characteristics at metal-silica interfaces remain unclear. In this study, we performed Density Functional Theory (DFT) calculations to study the hydrogen release mechanism at the typical Al/SiO2 metal-oxide interface. We found that interstitial hydrogen atoms can break interfacial Alsbnd Si bonds, passivating a Si sp3 orbital. Interstitial hydrogen atoms can also break interfacial Alsbnd O bonds, or be adsorbed at the interface on aluminum, forming stable Alsbnd Hsbnd Al bridges. We showed that hydrogenated Osbnd H, Sisbnd H and Alsbnd H bonds at the Al/SiO2 interfaces are polarized. The resulting bond dipole weakens the Osbnd H and Sisbnd H bonds, but strengthens the Alsbnd H bond under the application of a positive bias at the metal gate. Our calculations indicate that Alsbnd H bonds and Osbnd H bonds are more important than Sisbnd H bonds for the hydrogen release process.

Nanostructure, hydrogen bonding and rheology in choline chloride deep eutectic solvents as a function of the hydrogen bond donor.

PubMed

Stefanovic, Ryan; Ludwig, Michael; Webber, Grant B; Atkin, Rob; Page, Alister J

2017-01-25

Deep eutectic solvents (DESs) are a mixture of a salt and a molecular hydrogen bond donor, which form a eutectic liquid with a depressed melting point. Quantum mechanical molecular dynamics (QM/MD) simulations have been used to probe the 1 : 2 choline chloride-urea (ChCl : U), choline chloride-ethylene glycol (ChCl : EG) and choline chloride-glycerol (ChCl : Gly) DESs. DES nanostructure and interactions between the ions is used to rationalise differences in DES eutectic point temperatures and viscosity. Simulations show that the structure of the bulk hydrogen bond donor is largely preserved for hydroxyl based hydrogen bond donors (ChCl:Gly and ChCl:EG), resulting in a smaller melting point depression. By contrast, ChCl:U exhibits a well-established hydrogen bond network between the salt and hydrogen bond donor, leading to a larger melting point depression. This extensive hydrogen bond network in ChCl:U also leads to substantially higher viscosity, compared to ChCl:EG and ChCl:Gly. Of the two hydroxyl based DESs, ChCl:Gly also exhibits a higher viscosity than ChCl:EG. This is attributed to the over-saturation of hydrogen bond donor groups in the ChCl:Gly bulk, which leads to more extensive hydrogen bond donor self-interaction and hence higher cohesive forces within the bulk liquid.

Hydroxyl group as IR probe to detect the structure of ionic liquid-acetonitrile mixtures

NASA Astrophysics Data System (ADS)

Xu, Jing; Deng, Geng; Zhou, Yu; Ashraf, Hamad; Yu, Zhi-Wu

2018-06-01

Task-specific ionic liquids (ILs) are those with functional groups introduced in the cations or anions of ILs to bring about specific properties for various tasks. In this work, the hydrogen bonding interactions between a hydroxyl functionalized IL 1-(2-hydroxylethyl)-3-methylimidazolium tetrafluoroborate ([C2OHMIM][BF4]) and acetonitrile were investigated in detail by infrared spectroscopy, excess spectroscopy, two-dimensional correlation spectroscopy, combined with hydrogen nuclear magnetic resonance and density functional theory calculations (DFT). The hydroxyl group rather than C2sbnd H is found to be the main interaction site in the cation. And the ν(Osbnd H) is more sensitive than v(C-Hs) to the environment, which has been taken as an intrinsic probe to reflect the structural change of IL. Examining the region of ν(Osbnd H), by combining excess spectroscopy and DFT calculation, a number of species were identified in the mixtures. Other than the hydrogen bond between a cation and an anion, the hydroxyl group allows the formation of a hydrogen bond between two like-charged cations. The Osbnd H⋯O hydrogen bonding interactions in the hydroxyl-mediated cation-cation complexes are cooperative, while Osbnd H⋯F and C2sbnd H⋯F hydrogen bonding interactions in cation-anion complexes are anti-cooperative. These in-depth studies on the properties of the ionic liquid-acetonitrile mixtures may shed light on exploring their applications as mixed solvents and understanding the nature of doubly ionic hydrogen bonds.

Time-dependent vibrational spectral analysis of first principles trajectory of methylamine with wavelet transform.

PubMed

Biswas, Sohag; Mallik, Bhabani S

2017-04-12

The fluctuation dynamics of amine stretching frequencies, hydrogen bonds, dangling N-D bonds, and the orientation profile of the amine group of methylamine (MA) were investigated under ambient conditions by means of dispersion-corrected density functional theory-based first principles molecular dynamics (FPMD) simulations. Along with the dynamical properties, various equilibrium properties such as radial distribution function, spatial distribution function, combined radial and angular distribution functions and hydrogen bonding were also calculated. The instantaneous stretching frequencies of amine groups were obtained by wavelet transform of the trajectory obtained from FPMD simulations. The frequency-structure correlation reveals that the amine stretching frequency is weakly correlated with the nearest nitrogen-deuterium distance. The frequency-frequency correlation function has a short time scale of around 110 fs and a longer time scale of about 1.15 ps. It was found that the short time scale originates from the underdamped motion of intact hydrogen bonds of MA pairs. However, the long time scale of the vibrational spectral diffusion of N-D modes is determined by the overall dynamics of hydrogen bonds as well as the dangling ND groups and the inertial rotation of the amine group of the molecule.

Hydrogen bond disruption in DNA base pairs from (14)C transmutation.

PubMed

Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Christopher R; Mancera, Ricardo L; Marks, Nigel A

2014-09-04

Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that (14)C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these (14)C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication.

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides.

PubMed

Mphahlele, Malose Jack; Maluleka, Marole Maria; Rhyman, Lydia; Ramasami, Ponnadurai; Mampa, Richard Mokome

2017-01-04

The structures of the mono- and the dihalogenated N -unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide ( ABB ) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer ( A ) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

PubMed Central

Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

2015-01-01

Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner. PMID:26337527

Evaluating the potential for halogen bonding in ketosteroid isomerase’s oxyanion hole using unnatural amino acid mutagenesis

PubMed Central

Kraut, Daniel A; Churchil, Michael J; Dawson, Phillip E

2009-01-01

There has recently been an increasing interest in controlling macromolecular conformations and interactions through halogen bonding. Halogen bonds are favorable electrostatic interactions between polarized, electropositive chlorine, bromine or iodine atoms and electronegative atoms such as oxygen or nitrogen. These interactions have been likened to hydrogen bonds both in terms of their favored acceptor molecules, their geometries, and their energetics. We asked whether a halogen bond could replace a hydrogen bond in the oxyanion hole of ketosteroid isomerase, using semi-synthetic enzyme containing para-halogenated phenylalanine derivatives to replace the tyrosine hydrogen bond donor. Formation of a halogen bond to the oxyanion in the transition state would be expected to rescue the effects of mutation to phenylalanine, but all of the halogenated enzymes were comparable in activity to the phenylalanine mutant. We conclude that, at least in this active site, a halogen bond cannot functionally replace a hydrogen bond. PMID:19260691

Molecular interaction of (ethanol)2-water heterotrimers.

PubMed

Mejía, Sol M; Espinal, Juan F; Restrepo, Albeiro; Mondragón, Fanor

2007-08-23

The potential energy surface of the (ethanol)2-water heterotrimers for the trans and gauche conformers of ethanol was studied using density functional theory. The same approximation was used for characterizing representative clusters of (ethanol)3, (methanol)3, and (methanol)2-water. Trimerization energies and enthalpies as well as the analysis of geometric parameters suggest that the structures with a cyclic pattern in the three hydrogen bonds of the type O-H---O (primary hydrogen bonds), where all molecules are proton donor-acceptor at the same time, are more stable than those with just two primary hydrogen bonds. Additionally, we propose the formation of "secondary hydrogen bonds" between hydrogen atoms of the methyl group of ethanol and the oxygen atom of water or other ethanol molecule (C-H---O), which were found to be weaker than the primary hydrogen bonds.

Anion-assisted trans-cis isomerization of palladium(II) phosphine complexes containing acetanilide functionalities through hydrogen bonding interactions.

PubMed

Lu, Xiao-Xia; Tang, Hau-San; Ko, Chi-Chiu; Wong, Jenny Ka-Yan; Zhu, Nianyong; Yam, Vivian Wing-Wah

2005-03-28

The anion-assisted shift of trans-cis isomerization equilibrium of a palladium(II) complex containing acetanilide functionalities brought about by allosteric hydrogen bonding interactions has been established by UV/Vis, 1H NMR, 31P NMR and ESI-MS studies.

Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs

NASA Astrophysics Data System (ADS)

Zhou, Yu; Deng, Geng; Zheng, Yan-Zhen; Xu, Jing; Ashraf, Hamad; Yu, Zhi-Wu

2016-11-01

Cooperative behaviors of the hydrogen bonding networks in proteins have been discovered for a long time. The structural origin of this cooperativity, however, is still under debate. Here we report a new investigation combining excess infrared spectroscopy and density functional theory calculation on peptide analogs, represented by N-methylformamide (NMF) and N-methylacetamide (NMA). Interestingly, addition of the strong hydrogen bond acceptor, dimethyl sulfoxide, to the pure analogs caused opposite effects, namely red- and blue-shift of the N-H stretching infrared absorption in NMF and NMA, respectively. The contradiction can be reconciled by the marked lowering of the energy levels of the self-associates between NMA molecules due to a cooperative effect of the hydrogen bonds. On the contrary, NMF molecules cannot form long-chain cooperative hydrogen bonds because they tend to form dimers. Even more interestingly, we found excellent linear relationships between changes on bond orders of N-H/N-C/C = O and the hydrogen bond energy gains upon the formation of hydrogen bonding multimers in NMA, suggesting strongly that the cooperativity originates from resonance-assisted hydrogen bonds. Our findings provide insights on the structures of proteins and may also shed lights on the rational design of novel molecular recognition systems.

Probing for and Quantifying Agonist Hydrogen Bonds in α6β2 Nicotinic Acetylcholine Receptors.

PubMed

Post, Michael R; Lester, Henry A; Dougherty, Dennis A

2017-04-04

Designing subtype-selective agonists for neuronal nicotinic acetylcholine receptors is a challenging and significant goal aided by intricate knowledge of each subtype's binding patterns. We previously reported that in α6β2 receptors, acetylcholine makes a functional cation-π interaction with Trp149, but nicotine and TC299423 do not, suggesting a distinctive binding site. This work explores hydrogen binding at the backbone carbonyl associated with α6β2 Trp149. Substituting residue i + 1, Thr150, with its α-hydroxy analogue (Tah) attenuates the carbonyl's hydrogen bond accepting ability. At α6(T150Tah)β2, nicotine shows a 24-fold loss of function, TC299423 shows a modest loss, and acetylcholine shows no effect. Nicotine was further analyzed via a double-mutant cycle analysis utilizing N'-methylnicotinium, which indicated a hydrogen bond in α6β2 with a ΔΔG of 2.6 kcal/mol. Thus, even though nicotine does not make the conserved cation-π interaction with Trp149, it still makes a functional hydrogen bond to its associated backbone carbonyl.

Structure and Dynamics of Hydroxyl-Functionalized Protic Ammonium Carboxylate Ionic Liquids.

PubMed

Thummuru, Dhileep Nagi Reddy; Mallik, Bhabani S

2017-10-26

We performed classical molecular dynamics simulations to investigate the structure and dynamics of protic ionic liquids, 2-hydroxy ethylammonium acetate, ethylammonium hydroxyacetate, and 2-hydroxyethylammonium hydroxyacetate at ambient conditions. Structural properties such as density, radial distribution functions, spatial distribution functions, and structure factors have been calculated. Dynamic properties such as mean square displacements, as well as residence and hydrogen bond dynamics have also been calculated. Hydrogen bond lifetimes and residence times change with the addition of hydroxyl groups. We observe that when a hydroxyl group is present on the cation, dynamics become very slow and it forms a strong hydrogen bond with carboxylate oxygen atoms of the anion. The hydroxyl functionalized ILs show more dynamic diversity than structurally similar ILs.

Tuning Solvatochromism of Azo Dyes with Intramolecular Hydrogen Bonding in Solution and on Titanium Dioxide Nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Lei; Cole, Jacqueline M.; Liu, Xiaogang

2013-11-25

“Smart tuning” of optical properties in three azo dyes containing intramolecular hydrogen bonding is realized by the judicious control of solvents, when the dyes are in solution or adsorbed onto titanium dioxide nanoparticles. In solution, certain solvents destabilizing intramolecular hydrogen bonding induce a distinctive ≈70 nm “blue-shifted” absorption peak, compared with other solvents. In parallel, the optical properties of azo dye/TiO2 nanocomposites can be tuned using solvents with different hydrogen-bond accepting/donating abilities, giving insights into smart materials and dye-sensitized solar cell device design. It is proposed that intramolecular hydrogen bonding alone plays the leading role in such phenomena, which ismore » fundamentally different to other mechanisms, such as tautomerism and cis–trans isomerization, that explain the optical control of azo dyes. Hybrid density functional theory (DFT) is employed in order to trace the origin of this optical control, and these calculations support the mechanism involving intramolecular hydrogen bonding. Two complementary studies are also reported: 1H NMR spectroscopy is conducted in order to further understand the solvent effects on intramolecular hydrogen bonding; crystal structure analysis from associated research indicates the importance of intramolecular hydrogen bonding on intramolecular charge transfer.« less

Insight into hydrogen bonds and characterization of interlayer spacing of hydrated graphene oxide.

PubMed

Liu, Liyan; Zhang, Ruifeng; Liu, Ying; Tan, Wei; Zhu, Guorui

2018-05-28

The number of hydrogen bonds and detailed information on the interlayer spacing of graphene oxide (GO) confined water molecules were calculated through experiments and molecular dynamics simulations. Experiments play a crucial role in the modeling strategy and verification of the simulation results. The binding of GO and water molecules is essentially controlled by hydrogen bond networks involving functional groups and water molecules confined in the GO layers. With the increase in the water content, the clusters of water molecules are more evident. The water molecules bounding to GO layers are transformed to a free state, making the removal of water molecules from the system difficult at low water contents. The diffuse behaviors of the water molecules are more evident at high water contents. With an increase in the water content, the functional groups are surrounded by fewer water molecules, and the distance between the functional groups and water molecules increases. As a result, the water molecules adsorbed into the GO interlamination will enlarge the interlayer spacing. The interlayer spacing is also affected by the number of GO layers. These results were confirmed by the calculations of number of hydrogen bonds, water state, mean square displacement, radial distribution function, and interlayer spacing of hydrated GO. Graphical Abstract This work research the interaction between GO functional groups and confined water molecules. The state of water molecules and interlayer spacing of graphene oxide were proved to be related to the number of hydrogen bonds.

Bidentate, monoanionic auxiliary-directed functionalization of carbon-hydrogen bonds.

PubMed

Daugulis, Olafs; Roane, James; Tran, Ly Dieu

2015-04-21

In recent years, carbon-hydrogen bond functionalization has evolved from an organometallic curiosity to a tool used in mainstream applications in the synthesis of complex natural products and drugs. The use of C-H bonds as a transformable functional group is advantageous because these bonds are the most abundant functionality in organic molecules. One-step conversion of these bonds to the desired functionality shortens synthetic pathways, saving reagents, solvents, and labor. Less chemical waste is generated as well, showing that this chemistry is environmentally beneficial. This Account describes the development and use of bidentate, monoanionic auxiliaries for transition-metal-catalyzed C-H bond functionalization reactions. The chemistry was initially developed to overcome the limitations with palladium-catalyzed C-H bond functionalization assisted by monodentate directing groups. By the use of electron-rich bidentate directing groups, functionalization of unactivated sp(3) C-H bonds under palladium catalysis has been developed. Furthermore, a number of abundant base-metal complexes catalyze functionalization of sp(2) C-H bonds. At this point, aminoquinoline, picolinic acid, and related compounds are among the most used and versatile directing moieties in C-H bond functionalization chemistry. These groups facilitate catalytic functionalization of sp(2) and sp(3) C-H bonds by iron, cobalt, nickel, copper, ruthenium, rhodium, and palladium complexes. Exceptionally general reactivity is observed, enabling, among other transformations, direct arylation, alkylation, fluorination, sulfenylation, amination, etherification, carbonylation, and alkenylation of carbon-hydrogen bonds. The versatility of these auxilaries can be attributed to the following factors. First, they are capable of stabilizing high oxidation states of transition metals, thereby facilitating the C-H bond functionalization step. Second, the directing groups can be removed, enabling their use in synthesis and functionalization of natural products and medicinally relevant substances. While the development of these directing groups presents a significant advance, several limitations of this methodology are apparent. The use of expensive second-row transition metal catalysts is still required for efficient sp(3) C-H bond functionalization. Furthermore, the need to install and subsequently remove the relatively expensive directing group is a disadvantage.

Bidentate, Monoanionic Auxiliary-Directed Functionalization of Carbon–Hydrogen Bonds

PubMed Central

Daugulis, Olafs; Roane, James; Tran, Ly Dieu

2015-01-01

CONSPECTUS In recent years, carbon–hydrogen bond functionalization has evolved from an organometallic curiosity to mainstream applications in the synthesis of complex natural products and drugs. The use of C–H bonds as a transformable functional group is advantageous because these bonds are the most abundant functionality in organic molecules. One-step conversion of these bonds to the desired functionality shortens synthetic pathways, saving reagents, solvents, and labor. Less chemical waste is generated as well, showing that this chemistry is environmentally beneficial. This Account describes the development and use of bidentate, monoanionic auxiliaries for transition-metal-catalyzed C–H bond functionalization reactions. The chemistry was initially developed to overcome the limitations with palladium-catalyzed C–H bond functionalization assisted by monodentate directing groups. By the use of electron-rich bidentate directing groups, functionalization of unactivated sp3 C–H bonds under palladium catalysis has been developed. Furthermore, a number of abundant base-metal complexes catalyze functionalization of sp2 C–H bonds. At this point, aminoquinoline, picolinic acid, and related compounds are among the most used and versatile directing moieties in C–H bond functionalization chemistry. These groups facilitate catalytic functionalization of sp2 and sp3 C–H bonds by iron, cobalt, nickel, copper, ruthenium, rhodium, and palladium complexes. Exceptionally general reactivity is observed, enabling, among other transformations, direct arylation, alkylation, fluorination, sulfenylation, amination, etherification, carbonylation, and alkenylation of carbon–hydrogen bonds. The versatility of these auxilaries can be attributed to the following factors. First, they are capable of stabilizing high oxidation states of transition metals, thereby facilitating the C–H bond functionalization step. Second, the directing groups can be removed, enabling their use in synthesis and functionalization of natural products and medicinally relevant substances. While the development of these directing groups presents a significant advance, several limitations of this methodology are apparent. The use of expensive second-row transition metal catalysts is still required for efficient sp3 C–H bond functionalization. Furthermore, a disadvantage is the need to install and subsequently remove the relatively expensive directing group. PMID:25756616

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

2018-05-01

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

Periodic density functional theory study of ethylene hydrogenation over Co3O4 (1 1 1) surface: The critical role of oxygen vacancies

NASA Astrophysics Data System (ADS)

Lu, Jinhui; Song, JiaJia; Niu, Hongling; Pan, Lun; Zhang, Xiangwen; Wang, Li; Zou, Ji-Jun

2016-05-01

Recently, metal oxides are attracting increasing interests as hydrogenation catalyst. Herein we studied the hydrogenation of ethylene on perfect and oxygen defective Co3O4 (1 1 1) using periodic density functional theory. The energetics and pathways of ethylene hydrogenation to ethane were determined. We have demonstrated that (i) H2 dissociation on Co3O4 is a complicated two-step process through a heterolytic cleavage, followed by the migration of H atom and finally yields the homolytic product on both perfect and oxygen defective Co3O4 (1 1 1) surfaces easily. (ii) After introducing the surface oxygen vacancy, the stepwise hydrogenation of ethylene by atomic hydrogen is much easier than that on perfect surface due to the weaker bond strength of OH group. The strength of Osbnd H bond is a crucial factor for the hydrogenation reaction which involves the breakage of Osbnd H bond. The formation of oxygen vacancy increases the electronic charges at the adjacent surface O, which reduces its capability of further gaining electrons from adsorbed atomic hydrogen and then weakens the strength of Osbnd H bond. These results emphasize the importance of the oxygen vacancies for hydrogenation on metal oxides.

The change in hydrogen bond strength accompanying charge rearrangement: Implications for enzymatic catalysis

PubMed Central

Shan, Shu-ou; Herschlag, Daniel

1996-01-01

The equilibrium for formation of the intramolecular hydrogen bond (KHB) in a series of substituted salicylate monoanions was investigated as a function of ΔpKa, the difference between the pKa values of the hydrogen bond donor and acceptor, in both water and dimethyl sulfoxide. The dependence of log KHB upon ΔpKa is linear in both solvents, but is steeper in dimethyl sulfoxide (slope = 0.73) than in water (slope = 0.05). Thus, hydrogen bond strength can undergo substantially larger increases in nonaqueous media than aqueous solutions as the charge density on the donor or acceptor atom increases. These results support a general mechanism for enzymatic catalysis, in which hydrogen bonding to a substrate is strengthened as charge rearranges in going from the ground state to the transition state; the strengthening of the hydrogen bond would be greater in a nonaqueous enzymatic active site than in water, thus providing a rate enhancement for an enzymatic reaction relative to the solution reaction. We suggest that binding energy of an enzyme is used to fix the substrate in the low-dielectric active site, where the strengthening of the hydrogen bond in the course of a reaction is increased. PMID:8962076

Exactly solvable Schrödinger equation with double-well potential for hydrogen bond

NASA Astrophysics Data System (ADS)

Sitnitsky, A. E.

2017-05-01

We construct a double-well potential for which the Schrödinger equation can be exactly solved via reducing to the confluent Heun's one. Thus the wave function is expressed via the confluent Heun's function. The latter is tabulated in Maple so that the obtained solution is easily treated. The potential is infinite at the boundaries of the final interval that makes it to be highly suitable for modeling hydrogen bonds (both ordinary and low-barrier ones). We exemplify theoretical results by detailed treating the hydrogen bond in KHCO3 and show their good agreement with literature experimental data.

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Hydrogen-bond landscapes, geometry and energetics of squaric acid and its mono- and dianions: a Cambridge Structural Database, IsoStar and computational study.

PubMed

Allen, Frank H; Cruz-Cabeza, Aurora J; Wood, Peter A; Bardwell, David A

2013-10-01

As part of a programme of work to extend central-group coverage in the Cambridge Crystallographic Data Centre's (CCDC) IsoStar knowledge base of intermolecular interactions, we have studied the hydrogen-bonding abilities of squaric acid (H2SQ) and its mono- and dianions (HSQ(-) and SQ(2-)) using the Cambridge Structural Database (CSD) along with dispersion-corrected density functional theory (DFT-D) calculations for a range of hydrogen-bonded dimers. The -OH and -C=O groups of H2SQ, HSQ(-) and SQ(2-) are potent donors and acceptors, as indicated by their hydrogen-bond geometries in available crystal structures in the CSD, and by the attractive energies calculated for their dimers with acetone and methanol, which were used as model acceptors and donors. The two anions have sufficient examples in the CSD for their addition as new central groups in IsoStar. It is also shown that charge- and resonance-assisted hydrogen bonds involving H2SQ and HSQ(-) are similar in strength to those made by carboxylate COO(-) acceptors, while hydrogen bonds made by the dianion SQ(2-) are somewhat stronger. The study reinforces the value of squaric acid and its anions as cocrystal formers and their actual and potential importance as isosteric replacements for carboxylic acid and carboxylate functions.

Performance of Several Density Functional Theory Methods on Describing Hydrogen-Bond Interactions.

PubMed

Rao, Li; Ke, Hongwei; Fu, Gang; Xu, Xin; Yan, Yijing

2009-01-13

We have investigated eleven density functionals, including LDA, PBE, mPWPW91, TPSS, B3LYP, X3LYP, PBE0, O3LYP, B97-1, MPW1K, and TPSSh, for their performances on describing hydrogen bond (HB) interactions. The emphasis has been laid not only on their abilities to calculate the intermolecular hydrogen bonding energies but also on their performances in predicting the relative energies of intermolecular H-bonded complexes and the conformer stabilities due to intramolecular hydrogen bondings. As compared to the best theoretical values, we found that although PBE and PBE0 gave the best estimation of HB strengths, they might fail to predict the correct order of relative HB energies, which might lead to a wrong prediction of the global minimum for different conformers. TPSS and TPSSh did not always improve over PBE and PBE0. B3LYP was found to underestimate the intermolecular HB strengths but was among the best performers in calculating the relative HB energies. We showed here that X3LYP and B97-1 were able to give good values for both absolute HB strengths and relative HB energies, making these functionals good candidates for HB description.

The Effects of Hydrogen on the Potential-Energy Surface of Amorphous Silicon

NASA Astrophysics Data System (ADS)

Joly, Jean-Francois; Mousseau, Normand

2012-02-01

Hydrogenated amorphous silicon (a-Si:H) is an important semiconducting material used in many applications from solar cells to transistors. In 2010, Houssem et al. [1], using the open-ended saddle-point search method, ART nouveau, studied the characteristics of the potential energy landscape of a-Si as a function of relaxation. Here, we extend this study and follow the impact of hydrogen doping on the same a-Si models as a function of doping level. Hydrogen atoms are first attached to dangling bonds, then are positioned to relieve strained bonds of fivefold coordinated silicon atoms. Once these sites are saturated, further doping is achieved with a Monte-Carlo bond switching method that preserves coordination and reduces stress [2]. Bonded interactions are described with a modified Stillinger-Weber potential and non-bonded Si-H and H-H interactions with an adapted Slater-Buckingham potential. Large series of ART nouveau searches are initiated on each model, resulting in an extended catalogue of events that characterize the evolution of potential energy surface as a function of H-doping. [4pt] [1] Houssem et al., Phys Rev. Lett., 105, 045503 (2010)[0pt] [2] Mousseau et al., Phys Rev. B, 41, 3702 (1990)

Novel CDK inhibition profiles of structurally varied 1-aza-9-oxafluorenes.

PubMed

Voigt, Burkhardt; Meijer, Laurent; Lozach, Olivier; Schächtele, Christoph; Totzke, Frank; Hilgeroth, Andreas

2005-02-01

A series of 1-aza-9-oxafluorenes with functionally varied 3-substituents have been prepared from N-phenoxycarbonyl-4-phenyl-1,4-dihydropyridines and p-benzoquinone and biologically evaluated as inhibitors of various cyclin-dependant kinases. The absence of a 3-hydrogen bond acceptor function leads to a complete loss of inhibitory activity. Differing hydrogen bond acceptor functions surprisingly cause significant shifts in the selectivity of inhibition profiles.

Potential State-selective Hydrogen Bond Formation Can Modulate Activation and Desensitization of the α7 Nicotinic Acetylcholine Receptor*

PubMed Central

Wang, Jingyi; Papke, Roger L.; Stokes, Clare; Horenstein, Nicole A.

2012-01-01

A series of arylidene anabaseines were synthesized to probe the functional impact of hydrogen bonding on human α7 nicotinic acetylcholine receptor (nAChR) activation and desensitization. The aryl groups were either hydrogen bond acceptors (furans), donors (pyrroles), or neither (thiophenes). These compounds were tested against a series of point mutants of the ligand-binding domain residue Gln-57, a residue hypothesized to be proximate to the aryl group of the bound agonist and a putative hydrogen bonding partner. Q57K, Q57D, Q57E, and Q57L were chosen to remove the dual hydrogen bonding donor/acceptor ability of Gln-57 and replace it with hydrogen bond donating, hydrogen bond accepting, or nonhydrogen bonding ability. Activation of the receptor was compromised with hydrogen bonding mismatches, for example, pairing a pyrrole with Q57K or Q57L, or a furan anabaseine with Q57D or Q57E. Ligand co-applications with the positive allosteric modulator PNU-120596 produced significantly enhanced currents whose degree of enhancement was greater for 2-furans or -pyrroles than for their 3-substituted isomers, whereas the nonhydrogen bonding thiophenes failed to show this correlation. Interestingly, the PNU-120596 agonist co-application data revealed that for wild-type α7 nAChR, the 3-furan desensitized state was relatively stabilized compared with that of 2-furan, a reversal of the relationship observed with respect to the barrier for entry into the desensitized state. These data highlight the importance of hydrogen bonding on the receptor-ligand state, and suggest that it may be possible to fine-tune features of agonists that mediate state selection in the nAChR. PMID:22556416

NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids.

PubMed

Duchardt-Ferner, Elke; Wöhnert, Jens

2017-10-01

Hydrogen bonds involving the backbone phosphate groups occur with high frequency in functional RNA molecules. They are often found in well-characterized tertiary structural motifs presenting powerful probes for the rapid identification of these motifs for structure elucidation purposes. We have shown recently that stable hydrogen bonds to the phosphate backbone can in principle be detected by relatively simple NMR-experiments, providing the identity of both the donor hydrogen and the acceptor phosphorous within the same experiment (Duchardt-Ferner et al., Angew Chem Int Ed Engl 50:7927-7930, 2011). However, for imino and hydroxyl hydrogen bond donor groups rapidly exchanging with the solvent as well as amino groups broadened by conformational exchange experimental sensitivity is severely hampered by extensive line broadening. Here, we present improved methods for the rapid identification of hydrogen bonds to phosphate groups in nucleic acids by NMR. The introduction of the SOFAST technique into 1 H, 31 P-correlation experiments as well as a BEST-HNP experiment exploiting 3h J N,P rather than 2h J H,P coupling constants enables the rapid and sensitive identification of these hydrogen bonds in RNA. The experiments are applicable for larger RNAs (up to ~ 100-nt), for donor groups influenced by conformational exchange processes such as amino groups and for hydrogen bonds with rather labile hydrogens such as 2'-OH groups as well as for moderate sample concentrations. Interestingly, the size of the through-hydrogen bond scalar coupling constants depends not only on the type of the donor group but also on the structural context. The largest coupling constants were measured for hydrogen bonds involving the imino groups of protonated cytosine nucleotides as donors.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics.

PubMed

Brela, Mateusz Z; Boczar, Marek; Malec, Leszek M; Wójcik, Marek J; Nakajima, Takahito

2018-05-15

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers. Copyright © 2018 Elsevier B.V. All rights reserved.

Effect of characteristics of compounds on maintenance of an amorphous state in solid dispersion with crospovidone.

PubMed

Shibata, Yusuke; Fujii, Makiko; Kokudai, Makiko; Noda, Shinobu; Okada, Hideko; Kondoh, Masuo; Watanabe, Yoshiteru

2007-06-01

Solid dispersion (SD) of indomethacin with crospovidone (CrosPVP) shows useful characteristics for preparation of dosage forms. This study aimed to determine the types of drugs that could adopt a stable amorphous form in SD. Twenty compounds with various melting points (70-218 degrees C), molecular weights (135-504) and functional groups (amide, amino, carbonyl, hydroxyl, ketone etc.) were prepared in SD with CrosPVP. The CrosPVP SDs were prepared using a mechanical mixing and heating method. Melting point and molecular weight were found to have no influence on the ability of a compound to maintain an amorphous state in SD. All compounds containing hydrogen-bond-donor functional groups existed in an amorphous state in SD for at least 6 months. Infrared spectra suggested an interaction between the functional groups of these compounds and amide carbonyl group of CrosPVP. Compounds without hydrogen-bond-donor groups could not maintain an amorphous state and underwent recrystallization within 1 month. It was suggested that the presence of a hydrogen-bond-donor functional group in a compound is an important factor affecting the stable formation of SD with CrosPVP, which contains a hydrogen-bond acceptor.

Hydrogen bond strengthening between o-nitroaniline and formaldehyde in electronic excited states: A theoretical study

NASA Astrophysics Data System (ADS)

Yang, Juan; Li, An Yong

2018-06-01

To study the hydrogen bonds upon photoexcited, the time dependent density function method (TD DFT) was performed to investigate the excited state hydrogen bond properties of between o-nitroaniline (ONA) and formaldehyde (CH2O). The optimized structures of the complex and the monomers both in the ground state and the electronically excited states are calculated using DFT and TD DFT method respectively. Quantum chemical calculations of the electronic and vibrational absorption spectra are also carried out by TD DFT method at the different level. The complex ONA⋯CH2O forms the intramolecular hydrogen bond and intermolecular hydrogen bonds. Since the strength of hydrogen bonds can be measured by studying the vibrational absorption spectra of the characteristic groups on the hydrogen bonding acceptor and donor, it evidently confirms that the hydrogen bonds is strengthened in the S1/S2/T1 excited states upon photoexcitation. As a result, the hydrogen bonds cause that the CH stretch frequency of the proton donor CH2O has a blue shift, and the electron excitations leads to a frequency red shift of Ndbnd O and Nsbnd H stretch modes in the o-nitroaniline(ONA) and a small frequency blue shift of CH stretch mode in the formaldehyde(CH2O) in the S1 and S2 excited states. The excited states S1, S2 and T1 are locally excited states where only the ONA moiety is excited, but the CH2O moiety remains in its ground state.

Hydrogen bonding strength of diblock copolymers affects the self-assembled structures with octa-functionalized phenol POSS nanoparticles.

PubMed

Lu, Yi-Syuan; Yu, Chia-Yu; Lin, Yung-Chih; Kuo, Shiao-Wei

2016-02-28

In this study, the influence of the functional groups by the diblock copolymers of poly(styrene-b-4-vinylpyridine) (PS-b-P4VP), poly(styrene-b-2-vinylpyridine) (PS-b-P2VP), and poly(styrene-b-methyl methacrylate) (PS-b-PMMA) on their blends with octa-functionalized phenol polyhedral oligomeric silsesquioxane (OP-POSS) nanoparticles (NPs) was investigated. The relative hydrogen bonding strengths in these blends follow the order PS-b-P4VP/OP-POSS > PS-b-P2VP/OP-POSS > PS-b-PMMA/OP-POSS based on the Kwei equation from differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopic analyses. Small-angle X-ray scattering and transmission electron microscopic analyses show that the morphologies of the self-assembly structures are strongly dependent on the hydrogen bonding strength at relatively higher OP-POSS content. The PS-b-P4VP/OP-POSS hybrid complex system with the strongest hydrogen bonds shows the order-order transition from lamellae to cylinders and finally to body-centered cubic spheres upon increasing OP-POSS content. However, PS-b-P2VP/OP-POSS and PS-b-PMMA/OP-POSS hybrid complex systems, having relatively weaker hydrogen bonds, transformed from lamellae to cylinder structures at lower OP-POSS content (<50 wt%), but formed disordered structures at relatively high OP-POSS contents (>50 wt%).

The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

PubMed

Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

2010-09-02

The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

Variations of the Hydrogen Bonding and of the Hydrogen Bonded Network in Ethanol-Water Mixtures on Cooling.

PubMed

Pothoczki, Szilvia; Pusztai, Laszlo; Bako, Imre

2018-06-12

Molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20 and 30 mol % of the alcohol, at temperatures between room temperature and the experimental freezing point of the given mixture. All-atom type (OPLS) interatomic potentials have been assumed for ethanol, in combination with two kinds of rigid water models (SPC/E and TIP4P/2005). Both combinations have provided excellent reproductions of the experimental X-ray total structure factors at each temperature; this yielded a strong basis for further structural analyses. Beyond partial radial distribution functions, various descriptors of hydrogen bonded assemblies, as well as of the hydrogen bonded network have been determined. A clear tendency was observed towards that an increasing proportion of water molecules participate in hydrogen bonding with exactly 2 donor- and 2 acceptor sites as temperature decreases. Concerning larger assemblies held together by hydrogen bonding, the main focus was put on the properties of cyclic entities: it was found that, similarly to methanol-water mixtures, the number of hydrogen bonded rings has increased with lowering temperature. However, for ethanol-water mixtures the dominance of not the six-, but of the five-fold rings could be observed.

Intramolecular Hydrogen Bonding in Benzoxazines: When Structural Design Becomes Functional.

PubMed

Froimowicz, Pablo; Zhang, Kan; Ishida, Hatsuo

2016-02-18

The future evolution of benzoxazines and polybenzoxazines as advanced molecular, structural, functional, engineering, and newly commercial materials depends to a great extent on a deeper and more fundamental understanding at the molecular level. In this contribution, the field of benzoxazines is briefly introduced along with a more detailed review of ortho-amide-functional benzoxazines, which are the main subjects of this article. Provided in this article are the detailed and solid scientific evidences of intramolecular five-membered-ring hydrogen bonding, which is supposed to be responsible for the unique and characteristic features exhibited by this ever-growing family of ortho-functionalized benzoxazines. One-dimensional (1D) (1)H NMR spectroscopy was used to study various concentrations of benzoxazines in various solvents with different hydrogen-bonding capability and at various temperatures to investigate in detail the nature of hydrogen bonding in both ortho-amide-functionalized benzoxazine and its para counterpart. These materials were further investigated by two-dimensional (2D) (1)H-(1)H nuclear Overhauser effect spectroscopy (NOESY) to verify and support the conclusions derived during the 1D (1)H NMR experiments. Only highly purified single-crystal benzoxazine samples have been used for this study to avoid additional interactions caused by any impurities. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermodynamics of hydrogen bond patterns in supramolecular assemblies of water molecules.

PubMed

Henry, Marc

2002-07-02

The PACHA (Partial Atomic Charges and Hardnesses Analysis) formalism is applied to various supramolecular assemblies of water molecules. After a detailed study of all available crystal structures for ice polymorphs, we shown that the hydrogen bond strength is roughly constant below 1 GPa and considerably weakened above that value. New hydrogen bond patterns are proposed for ice IV, V, and VI after (EB) (electrostatic balance) minimization. For other polymorphs, there is an almost perfect coincidence between experimental and predicted hydrogen bond patterns. The evolution of hydrogen bond energy as a function of molecular geometry in water clusters with up to 280 water molecules and in large supramolecular compounds is quantitatively described. Intermolecular hydrogen bonds are found to lie between -9 and -32 kJ mol-1, the stronger interaction occurs within the spherical fully disordered water droplet buried at the heart of Müller's superfullerene keplerate. The weakest one occurs in a chiral molecular snub cube built from six calix[4]resorcinarene and eight water molecules. Intramolecular hydrogen bonds are found in the range -10-100 kJ mol-1 and can thus be considerably stronger than intermolecular bonds. Finally, through the investigation of a clathrate type I compound, it was possible to obtain a deep insight of the host-guest interactions and self-assembly rules of water cages in these materials.

An X-ray crystallographic and density functional theory study of (3Z)-4-(5-ethylsulfonyl-2-hydroxyanilino)pent-3-en-2-one and (3Z)-4-(5-tert-butyl-2-hydroxyanilino)pent-3-en-2-one.

PubMed

Akerman, Kate J; Munro, Orde Q

2013-03-01

The Schiff base enaminones (3Z)-4-(5-ethylsulfonyl-2-hydroxyanilino)pent-3-en-2-one, C13H17NO4S, (I), and (3Z)-4-(5-tert-butyl-2-hydroxyanilino)pent-3-en-2-one, C15H21NO2, (II), were studied by X-ray crystallography and density functional theory (DFT). Although the keto tautomer of these compounds is dominant, the O=C-C=C-N bond lengths are consistent with some electron delocalization and partial enol character. Both (I) and (II) are nonplanar, with the amino-phenol group canted relative to the rest of the molecule; the twist about the N(enamine)-C(aryl) bond leads to dihedral angles of 40.5 (2) and -116.7 (1)° for (I) and (II), respectively. Compound (I) has a bifurcated intramolecular hydrogen bond between the N-H group and the flanking carbonyl and hydroxy O atoms, as well as an intermolecular hydrogen bond, leading to an infinite one-dimensional hydrogen-bonded chain. Compound (II) has one intramolecular hydrogen bond and one intermolecular C=O...H-O hydrogen bond, and consequently also forms a one-dimensional hydrogen-bonded chain. The DFT-calculated structures [in vacuo, B3LYP/6-311G(d,p) level] for the keto tautomers compare favourably with the X-ray crystal structures of (I) and (II), confirming the dominance of the keto tautomer. The simulations indicate that the keto tautomers are 20.55 and 18.86 kJ mol(-1) lower in energy than the enol tautomers for (I) and (II), respectively.

An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States†.

PubMed

Gatti, Carlo; Macetti, Giovanni; Boyd, Russell J; Matta, Chérif F

2018-07-05

The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Hydrogen Bonding: Between Strengthening the Crystal Packing and Improving Solubility of Three Haloperidol Derivatives.

PubMed

Saluja, Hardeep; Mehanna, Ahmed; Panicucci, Riccardo; Atef, Eman

2016-06-01

The purpose of this study is to confirm the impact of polar functional groups on inter and intra-molecular hydrogen bonding in haloperidol (HP) and droperidol (DP) and, hence, their effects on dissolution using a new approach. To confirm our theory, a new molecule: deshydroxy-haloperidol (DHP) was designed and its synthesis was requested from a contract laboratory. The molecule was then studied and compared to DP and HP. Unlike DHP, both the HP and DP molecules have hydrogen donor groups, therefore, DHP was used to confirm the relative effects of the hydrogen donor group on solubility and crystal packing. The solid dispersions of the three structurally related molecules: HP, DP, and DHP were prepared using PVPK30, and characterized using XRPD and IR. A comparative dissolution study was carried out in aqueous medium. The absence of a hydrogen bonding donor group in DHP resulted in an unexpected increase in its aqueous solubility and dissolution rate from solid dispersion, which is attributed to weaker crystal pack. The increased dissolution rate of HP and DP from solid dispersions is attributed to drug-polymer hydrogen bonding that interferes with the drug-drug intermolecular hydrogen bonding and provides thermodynamic stability of the dispersed drug molecules. The drug-drug intermolecular hydrogen bond is the driving force for precipitation and crystal packing.

Electron transfer across multiple hydrogen bonds: the case of ureapyrimidinedione-substituted vinyl ruthenium and osmium complexes.

PubMed

Pichlmaier, Markus; Winter, Rainer F; Zabel, Manfred; Zális, Stanislav

2009-04-08

Ruthenium and osmium complexes 2a,b and 3a,b featuring the N-4,6-dioxo-5,5-dibutyl- or the N-4,6-dioxo-5,5-di-(2-propenyl)-1,4,5,6-tetrahydropyrimidin-2-yl-N'(4-ethenylphenyl)-urea ligand dimerize by a self-complementary quadruply hydrogen-bonding donor/donor/acceptor/acceptor (DDAA) motif. We provide evidence that the dimeric structures are maintained in nonpolar solvents and in 0.1 M NBu(4)PF(6)/CH(2)Cl(2) supporting electrolyte solution. All complexes are reversibly oxidized in two consecutive two-electron oxidations (DeltaE(1/2) approximately = 500 mV) without any discernible potential splitting for the oxidation of the individual hydrogen-bridged redox active moieties. IR and UV/vis/NIR spectroelectrochemistry show a one-step conversion of the neutral to the dication without any discernible features of an intermediate monooxidized radical cation. Oxidation-induced IR changes of the NH and CO groups that are involved in hydrogen bonding are restricted to the styryl-bonded urea NH function. IR band assignments are aided by quantum chemical calculations. Our experimental findings clearly show that, at least in the present systems, the ureapyrimidinedione (Upy) DDAA hydrogen-bonding motif does not support electron transfer. The apparent reason is that neither of the hydrogen-bonding functionalities contributes to the occupied frontier levels. This results in nearly degenerate pairs of MOs representing the in-phase and out-of-phase combinations of the individual monomeric building blocks.

IR + VUV double resonance spectroscopy and extended density functional theory studies of ketone solvation by alcohol: 2-butanone·(methanol)n, n = 1-4 clusters.

PubMed

Shin, Joong-Won; Bernstein, Elliot R

2017-09-28

Infrared plus vacuum ultraviolet (IR + VUV) photoionization vibrational spectroscopy of 2-butanone/methanol clusters [MEK·(MeOH) n , n = 1-4] is performed to explore structures associated with hydrogen bonding of MeOH molecules to the carbonyl functional group of the ketone. IR spectra and X3LYP/6-31++G(d,p) calculations show that multiple isomers of MEK·(MeOH) n are generated in the molecular beam as a result of several hydrogen bonding sites available to the clusters throughout the size range investigated. Isomer interconversion involving solvating MeOH rearrangement should probably occur for n = 1 and 2. The mode energy for a hydrogen bonded OH stretching transition gradually redshifts as the cluster size increases. Calculations suggest that the n = 3 cluster isomers adopt structures in which the MEK molecule is inserted into the cyclic MeOH hydrogen bond network. In larger structures, the cyclic network may be preserved.

Density functional theory meta-GGA + U study of water incorporation in the metal-organic framework material Cu-BTC.

PubMed

Cockayne, Eric; Nelson, Eric B

2015-07-14

Water absorption in the metal-organic framework (MOF) material Cu-BTC, up to a concentration of 3.5 H2O per Cu ion, is studied via density functional theory at the meta-GGA + U level. The stable arrangements of water molecules show chains of hydrogen-bonded water molecules and a tendency to form closed cages at high concentration. Water clusters are stabilized primarily by a combination of water-water hydrogen bonding and Cu-water oxygen interactions. Stability is further enhanced by van der Waals interactions, electric field enhancement of water-water bonding, and hydrogen bonding of water to framework oxygens. We hypothesize that the tendency to form such stable clusters explains the particularly strong affinity of water to Cu-BTC and related MOFs with exposed metal sites.

Performance of wave function and density functional methods for water hydrogen bond spin-spin coupling constants.

PubMed

García de la Vega, J M; Omar, S; San Fabián, J

2017-04-01

Spin-spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob's ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict 1 J O H , 2 J H H and 2h J O O couplings, while 1h J O H is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for 1 J O H and 2 J H H have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods. Graphical Abstract Evaluation of the additive effect of the hydrogen bond on spin-spin coupling constants of water using WF and DFT methods.

Hydrogen bond docking preference in furans: Osbnd H ⋯ π vs. Osbnd H ⋯ O

NASA Astrophysics Data System (ADS)

Jiang, Xiaotong; Tsona, Narcisse T.; Tang, Shanshan; Du, Lin

2018-02-01

The docking sites of hydrogen bonds in complexes formed between 2,2,2-trifluoroethanol (TFE), furan (Fu), and 2-methyl furan (MF) have been investigated. Using density functional theory (DFT) calculations, gas phase and matrix isolation FTIR spectroscopies, the strengths of Osbnd H ⋯ O and Osbnd H ⋯ π hydrogen bonds in the complexes were compared to find the docking preference. Calculations suggest that the hydrogen bond donor, TFE, is more likely to dock onto the oxygen atom of the aromatic furans ring, and consequently, the Osbnd H ⋯ O type hydrogen bond is relatively stronger than the Osbnd H ⋯ π type. The FTIR spectrum in the OH-stretching fundamental range obtained at room temperatures has been compared with that obtained at extremely low temperatures in the matrix. The fundamental and the red shifts of OH-stretching vibrations were observed in both FTIR spectra, confirming the formation of hydrogen bonded complexes. By assessing the ability of furan and MF to participate in the formation of Osbnd H ⋯ O hydrogen bond, the effect of ring methylation has been highlighted. From the calculated geometric and thermodynamic parameters as well as the frequency shift of the OH-stretching vibrations in complexes, TFE-MF is found to be more stable than TFE-Fu, which suggests that the strength of the Osbnd H ⋯ O hydrogen bond in TFE-MF originates from the high activity of the furan molecule caused by the methylation of the aromatic ring. The present study furthers the knowledge of docking preference in heteroaromatic molecules and is helpful to understand the nature of intermolecular interactions between hydrogen bond donors and acceptors, including both electron-deficient atoms and π cloud.

Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Strate, Anne; Neumann, Jan; Overbeck, Viviane; Bonsa, Anne-Marie; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf

2018-05-01

We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of hydrogen-bonded ion pairs in these ionic liquids.

Hydrogen bonding donation of N-methylformamide with dimethylsulfoxide and water

NASA Astrophysics Data System (ADS)

Borges, Alexandre; Cordeiro, João M. M.

2013-04-01

20% N-methylformamide (NMF) mixtures with water and with dimethylsulfoxide (DMSO) have been studied. A comparison between the hydrogen bonding (H-bond) donation of N-methylformamide with both solvents in the mixtures is presented. Results of radial distribution functions, pair distribution energies, molecular dipole moment correlation, and geometry of the H-bonded species in each case are shown. The results indicate that the NMF - solvent H-bond is significantly stronger with DMSO than with water. The solvation shell is best organized in the DMSO mixture than in the aqueous one.

The stability of cellulose: a statistical perspective from a coarse-grained model of hydrogen-bond networks.

PubMed

Shen, Tongye; Gnanakaran, S

2009-04-22

A critical roadblock to the production of biofuels from lignocellulosic biomass is the efficient degradation of crystalline microfibrils of cellulose to glucose. A microscopic understanding of how different physical conditions affect the overall stability of the crystalline structure of microfibrils could facilitate the design of more effective protocols for their degradation. One of the essential physical interactions that stabilizes microfibrils is a network of hydrogen (H) bonds: both intrachain H-bonds between neighboring monomers of a single cellulose polymer chain and interchain H-bonds between adjacent chains. We construct a statistical mechanical model of cellulose assembly at the resolution of explicit hydrogen-bond networks. Using the transfer matrix method, the partition function and the subsequent statistical properties are evaluated. With the help of this lattice-based model, we capture the plasticity of the H-bond network in cellulose due to frustration and redundancy in the placement of H-bonds. This plasticity is responsible for the stability of cellulose over a wide range of temperatures. Stable intrachain and interchain H-bonds are identified as a function of temperature that could possibly be manipulated toward rational destruction of crystalline cellulose.

Structural characteristics of hydrated protons in the conductive channels: effects of confinement and fluorination studied by molecular dynamics simulation.

PubMed

Zhang, Ning; Song, Yuechun; Ruan, Xuehua; Yan, Xiaoming; Liu, Zhao; Shen, Zhuanglin; Wu, Xuemei; He, Gaohong

2016-09-21

The relationship between the proton conductive channel and the hydrated proton structure is of significant importance for understanding the deformed hydrogen bonding network of the confined protons which matches the nanochannel. In general, the structure of hydrated protons in the nanochannel of the proton exchange membrane is affected by several factors. To investigate the independent effect of each factor, it is necessary to eliminate the interference of other factors. In this paper, a one-dimensional carbon nanotube decorated with fluorine was built to investigate the independent effects of nanoscale confinement and fluorination on the structural properties of hydrated protons in the nanochannel using classical molecular dynamics simulation. In order to characterize the structure of hydrated protons confined in the channel, the hydrogen bonding interaction between water and the hydrated protons has been studied according to suitable hydrogen bond criteria. The hydrogen bond criteria were proposed based on the radial distribution function, angle distribution and pair-potential energy distribution. It was found that fluorination leads to an ordered hydrogen bonding structure of the hydrated protons near the channel surface, and confinement weakens the formation of the bifurcated hydrogen bonds in the radial direction. Besides, fluorination lowers the free energy barrier of hydronium along the nanochannel, but slightly increases the barrier for water. This leads to disintegration of the sequential hydrogen bond network in the fluorinated CNTs with small size. In the fluorinated CNTs with large diameter, the lower degree of confinement produces a spiral-like sequential hydrogen bond network with few bifurcated hydrogen bonds in the central region. This structure might promote unidirectional proton transfer along the channel without random movement. This study provides the cooperative effect of confinement dimension and fluorination on the structure and hydrogen bonding of the slightly acidic water in the nanoscale channel.

A highly directional fourfold hydrogen-bonding motif for supramolecular structures through self-assembly of fullerodendrimers.

PubMed

Hahn, Uwe; González, Juan J; Huerta, Elisa; Segura, Margarita; Eckert, Jean-François; Cardinali, François; de Mendoza, Javier; Nierengarten, Jean-François

2005-11-04

Supramolecular dendrimers resulting from the dimerization of fullerene-functionalized dendrons through a quadruple hydrogen-bonding motif were prepared. The synthetic strategy is based on the esterification of a tert-butoxycarbonyl (Boc)-protected 2-ureido-4-[1H]pyrimidinone precursor possessing an alcohol function with fullerodendrons bearing a carboxylic acid unit at the focal point. Subsequent acidic treatment to cleave the protecting group and reaction of the resulting amine with octylisocyanate affords the targeted compounds. As demonstrated by the results of MALDI-TOF mass spectrometry and 1H NMR spectroscopy, both of the 2-ureido-4-[1H]pyrimidinone derivatives form self-assembled dimers spontaneously through hydrogen-bonding interactions, thus leading to supramolecular structures containing two or ten fullerene moieties.

Chemical bonding analysis on amphoteric hydrogen - alkaline earth ammine borohydrides

NASA Astrophysics Data System (ADS)

Kiruthika, S.; Ravindran, P.

2018-04-01

Usually the ions in solid are in the positive oxidation states or in the negative oxidation state depending upon the chemical environment. It is highly unusual for an ion having both positive as well as negative oxidation state in a particular compound. Structural analysis suggest that the alkaline earth ammine borohydrides (AABH) with the chemical formula M (BH4)2(NH3)2 (M = Mg, Ca, or Sr) where hydrogen is present in +1 and -1 oxidation states. In order to understand the oxidation states of hydrogen and also the character of chemical bond present in AABH we have made charge density, electron localization function, Born effective charge, Bader effective charge, and density of states analyses using result from the density functional calculations. Our detailed analyses show that hydrogen is in amphoteric behavior with hydrogen closer to boron is in negative oxidation state and that closer to nitrogen is in the positive oxidation state. Due to the presence of finite covalent bonding between the consitutents in AABH the oxidation state of hydrogen is non-interger value. The confirmation of the presence of amphtoric behavior of hydrogen in AABH has implication in hydrogen storage applications.

TDDFT study of twisted intramolecular charge transfer and intermolecular double proton transfer in the excited state of 4‧-dimethylaminoflavonol in ethanol solvent

NASA Astrophysics Data System (ADS)

Wang, Ye; Shi, Ying; Cong, Lin; Li, Hui

2015-02-01

Time-dependent density functional theory method at the def-TZVP/B3LYP level was employed to investigate the intramolecular and intermolecular hydrogen bonding dynamics in the first excited (S1) state of 4‧-dimethylaminoflavonol (DMAF) monomer and in ethanol solution. In the DMAF monomer, we demonstrated that the intramolecular charge transfer (ICT) takes place in the S1 state. This excited state ICT process was followed by intramolecular proton transfer. Our calculated results are in good agreement with the mechanism proposed in experimental work. For the hydrogen-bonded DMAF-EtOH complex, it was demonstrated that the intermolecular hydrogen bonds can induce the formation of the twisted intramolecular charge transfer (TICT) state and the conformational twisting is along the C3-C4 bond. Moreover, the intermolecular hydrogen bonds can also facilitate the intermolecular double proton transfer in the TICT state. A stepwise intermolecular double proton transfer process was revealed. Therefore, the intermolecular hydrogen bonds can alter the mechanism of intramolecular charge transfer and proton transfer in the excited state for the DMAF molecule.

XRD, vibrational spectra and quantum chemical studies of an anticancer drug: 6-Mercaptopurine.

PubMed

Kumar, S Suresh; Athimoolam, S; Sridhar, B

2015-07-05

The single crystal of the hydrated anticancer drug, 6-Mercaptopurine (6-MP), has been grown by slow evaporation technique under room temperature. The structure was determined by single crystal X-ray diffraction. The vibrational spectral analysis was carried out using Laser Raman and FT-IR spectroscopy in the range of 3300-100 and 4000-400 cm(-1). The single crystal X-ray studies shows that the crystal packing is dominated by N-H⋯O and O-H⋯N classical hydrogen bonds leading to a hydrogen bonded ensemble. This classical hydrogen bonds were further connected through O-H⋯S hydrogen bond to form two primary ring R4(4)(16) and R4(4)(12) motifs. These two primary ring motifs are interlinked with each other to build a ladder like structure. These ladders are connected through N-H⋯N hydrogen bond along c-axis of the unit cell through chain C(5) motifs. Further, the strength of the hydrogen bonds is studied through vibrational spectral measurements. The shifting of bands due to the intermolecular interactions was also analyzed in the solid crystalline state. Geometrical optimizations of the drug molecule were done by Density Functional Theory (DFT) using the B3LYP function and Hartree-Fock (HF) level with 6-311++G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which show significant agreement. The natural bond orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and intramolecular charge transfer (ICT). The chemical hardness, electro-negativity and chemical potential of the molecule are carried out by HOMO-LUMO plot. In which, the frontier orbitals has lower band gap value indicating the possible pharmaceutical activity of the molecule. Copyright © 2015 Elsevier B.V. All rights reserved.

Structures and interactions in N-methylacetamide-water mixtures studied by IR spectra and density functional theory

NASA Astrophysics Data System (ADS)

Zhang, Rong; Li, Haoran; Lei, Yi; Han, Shijun

2004-05-01

IR spectra have been performed to study the structures and interactions in N-methylacetamide and water mixtures. Because of the competitions of acceptor and donor of the strong hydrogen bonds, some interesting phenomena of red shifts and blue shifts are observed in νCO and νN-H. It is due to the blue-shifting C-H⋯O hydrogen bond, the νC-H blue shifts more obviously. Then some representative cluster structures are suggested and further investigated by density functional theory method. The changes in bond length and frequency shift of the structures give good reasons for the red shift and blue shift, which represents excellent agreement with the IR experiment. The investigations of IR spectra and DFT calculations reveal that the weak C-H⋯O interactions play different roles compared with the classical strong hydrogen bonds in the NMA-water mixtures.

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

PubMed

Maguire, Jack B; Boyken, Scott E; Baker, David; Kuhlman, Brian

2018-05-08

Hydrogen bond networks play a critical role in determining the stability and specificity of biomolecular complexes, and the ability to design such networks is important for engineering novel structures, interactions, and enzymes. One key feature of hydrogen bond networks that makes them difficult to rationally engineer is that they are highly cooperative and are not energetically favorable until the hydrogen bonding potential has been satisfied for all buried polar groups in the network. Existing computational methods for protein design are ill-equipped for creating these highly cooperative networks because they rely on energy functions and sampling strategies that are focused on pairwise interactions. To enable the design of complex hydrogen bond networks, we have developed a new sampling protocol in the molecular modeling program Rosetta that explicitly searches for sets of amino acid mutations that can form self-contained hydrogen bond networks. For a given set of designable residues, the protocol often identifies many alternative sets of mutations/networks, and we show that it can readily be applied to large sets of residues at protein-protein interfaces or in the interior of proteins. The protocol builds on a recently developed method in Rosetta for designing hydrogen bond networks that has been experimentally validated for small symmetric systems but was not extensible to many larger protein structures and complexes. The sampling protocol we describe here not only recapitulates previously validated designs with performance improvements but also yields viable hydrogen bond networks for cases where the previous method fails, such as the design of large, asymmetric interfaces relevant to engineering protein-based therapeutics.

The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site.

PubMed

DeChancie, Jason; Houk, K N

2007-05-02

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each--NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin-bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.

The unique functional role of the C-HS hydrogen bond in the substrate specificity and enzyme catalysis of type 1 methionine aminopeptidase.

PubMed

Reddi, Ravikumar; Singarapu, Kiran Kumar; Pal, Debnath; Addlagatta, Anthony

2016-07-19

It is intriguing how nature attains recognition specificity between molecular interfaces where there is no apparent scope for classical hydrogen bonding or polar interactions. Methionine aminopeptidase (MetAP) is one such enzyme where this fascinating conundrum is at play. In this study, we demonstrate that a unique C-HS hydrogen bond exists between the enzyme methionine aminopeptidase (MetAP) and its N-terminal-methionine polypeptide substrate, which allows specific interaction between apparent apolar interfaces, imposing a strict substrate recognition specificity and efficient catalysis, a feature replicated in Type I MetAPs across all kingdoms of life. We evidence this evolutionarily conserved C-HS hydrogen bond through enzyme assays on wild-type and mutant MetAP proteins from Mycobacterium tuberculosis that show a drastic difference in catalytic efficiency. The X-ray crystallographic structure of the methionine bound protein revealed a conserved water bridge and short contacts involving the Met side-chain, a feature also observed in MetAPs from other organisms. Thermal shift assays showed a remarkable 3.3 °C increase in melting temperature for methionine bound protein compared to its norleucine homolog, where C-HS interaction is absent. The presence of C-HS hydrogen bonding was also corroborated by nuclear magnetic resonance spectroscopy through a change in chemical shift. Computational chemistry studies revealed the unique role of the electrostatic environment in facilitating the C-HS interaction. The significance of this atypical hydrogen bond is underscored by the fact that the function of MetAP is essential for any living cell.

An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

NASA Technical Reports Server (NTRS)

Jackels, C. F.

1985-01-01

Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

From flavoenzymes to devices: The role of electronic effects in recognition

NASA Astrophysics Data System (ADS)

Deans, Robert

Acylated aminopyridines provide models for specific flavoenzyme-cofactor interactions, allowing isolation and observation of the effects of hydrogen bonding on flavin NMR. To determine the relative hydrogen bond affinities of O(2) and O(4) of the flavin, a 2-aminopyridine based receptor was investigated. Additionally, this receptor allowed the effects of hydrogen bonding at O(2) and O(4) on the electron distribution in the flavin nucleus to be determined using sp{13}C NMR. A new family of receptors for flavins based on 6-aryl-2,4-(acyldiamino)-s-triazines was synthesized. In these synthetic hosts, systematic variation of the spatially remote substituents on the 6-aryl ring altered the hydrogen bond donating abilities of the amide functionality and the hydrogen bond accepting properties of the triazine N(3). This variation resulted in a strong modulation of the efficiency of flavin binding, with association constants for the receptor flavin complexes ranging over an 8-fold range. In addition, the communication of electronic information over extended distances was also investigated. Polymers can provide relevant media for the modeling of biological processes, including molecular recognition. To explore this possibility, a diaminotriazine-functionalized polymer was synthesized, starting from Merrifield's peptide resin. This polymer selectively bound a flavin derivative through hydrogen bonding, efficiently extracting it from a chloroform solution, as monitored by UV-vis extraction studies. The temperature profile of this polymer-flavin binding was also investigated and compared to the analogous solution-phase triazine-flavin dyad. Hydrogen bonding and aromatic stacking are fundamental interactions in molecular recognition. These interactions are sensitive to the redox states of the components of the host-guest complex. To explore the interplay of recognition and redox processes, a system consisting of two hosts and one guest, where guest binding interactions (hydrogen bonding and aromatic stacking) were modulated via choice of redox state was examined. Proper choice of receptors then provided a device where the competition between the two hosts was controlled by the redox state of the guest. The efficient reversal of host preference in this assembly provided an electrochemically-controlled three-component, two-pole, molecular switch.

Hydrogen-bond dynamics at the bio-water interface in hydrated proteins: a molecular-dynamics study.

PubMed

Nandi, Prithwish K; English, Niall J; Futera, Zdenek; Benedetto, Antonio

2016-12-21

Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions. Here, we present a molecular-dynamics-simulation study on a solvated model protein (hen egg-white lysozyme), in which we determine, inter alia, the relaxation dynamics of the hydrogen-bond network between the protein and its hydration water molecules on a residue-per-residue basis. Hydrogen-bond breakage/formation kinetics is rather heterogeneous in temperature dependence (due to the heterogeneity of the free-energy surface), and is driven by the magnitude of thermal motions of various different protein residues which provide enough thermal energy to overcome energy barriers to rupture their respective hydrogen bonds with water. In particular, arginine residues exhibit the highest number of such hydrogen bonds at low temperatures, losing almost completely such bonding above 230 K. This suggests that hydration water's dynamical crossover, observed experimentally for hydrated lysozymes at ∼220 K, lies not at the origin of the protein residues' larger-amplitude motions, but rather arises as a consequence thereof. This highlights the need for new experimental investigations, and new interpretations to link protein dynamics to functions, in the context of key interrelationships with the solvation layer.

Amide-Directed Photoredox Catalyzed C-C Bond Formation at Unactivated sp3 C-H Bonds

PubMed Central

Chu, John C. K.; Rovis, Tomislav

2017-01-01

Carbon-carbon (C-C) bond formation is paramount in the synthesis of biologically relevant molecules, modern synthetic materials and commodity chemicals such as fuels and lubricants. Traditionally, the presence of a functional group is required at the site of C-C bond formation. Strategies that allow C-C bond formation at inert carbon-hydrogen (C-H) bonds allow scientists to access molecules which would otherwise be inaccessible and to develop more efficient syntheses of complex molecules.1,2 Herein we report a method for the formation of C-C bonds by directed cleavage of traditionally non-reactive C-H bonds and their subsequent coupling with readily available alkenes. Our methodology allows for the selective C-C bond formation at single C-H bonds in molecules that contain a multitude of seemingly indifferentiable such bonds. Selectivity arises through a relayed photoredox catalyzed oxidation of an N-H bond. We anticipate our findings to serve as a starting point for functionalization at inert C-H bonds through a hydrogen atom transfer strategy. PMID:27732580

Crystal structure of rivastigmine hydrogen tartrate Form I (Exelon®), C 14H 23N 2O 2(C 4H 5O 6)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaduk, James A.; Zhong, Kai; Gindhart, Amy M.

2016-03-08

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 groupP2 1(#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) Å 3, 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 bondsmore » 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.« less

Formation of solvate structures by the ortho-, meta-, and para-isomers of hydroxybenzoic acid in supercritical fluid

NASA Astrophysics Data System (ADS)

Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.; Petrenko, V. E.

2017-04-01

The solvate structures formed by the ortho-, meta-, and para-isomers of hydroxybenzoic acid ( o-HBA, m-HBA, and p-HBA) with a polar co-solvent (methanol at a concentration of 0.030 and 0.035 mole fractions) in supercritical carbon dioxide at a constant density of 0.7 g/cm3 and temperatures of 318 and 328 K have been studied by the classic molecular dynamics. It has been determined that a stable hydrogen-bonded complex with the co-solvent forms via the hydrogen of the carboxyl group for all isomers. The probability of this complex existence is high at all temperatures and concentrations. In the o-HBA molecule, the other functional groups are engaged in the intramolecular hydrogen bond, but not involved in interactions with methanol. It has been found that m-HBA and p-HBA can be involved in hydrogen bonds with methanol via hydroxyl hydrogen and oxygen atoms; they are characterized by the presence of one more co-solvent molecule (rarely, two molecules) in their solvation shell and intermittent formations/breakages of hydrogen bonds via other functional groups. These bonds are far less stable, and their formation is sensitive to change of temperature and co-solvent concentration. It has been concluded that the degree of selective solvation of m-HBA and p-HBA by co-solvent molecules is approximately the same, but the rate of structural rearrangements in the nearest environment of m-HBA is higher than that of p-HBA.

Stretched hydrogen molecule from a constrained-search density-functional perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valone, Steven M; Levy, Mel

2009-01-01

Constrained-search density functional theory gives valuable insights into the fundamentals of density functional theory. It provides exact results and bounds on the ground- and excited-state density functionals. An important advantage of the theory is that it gives guidance in the construction of functionals. Here they engage constrained search theory to explore issues associated with the functional behavior of 'stretched bonds' in molecular hydrogen. A constrained search is performed with familiar valence bond wavefunctions ordinarily used to describe molecular hydrogen. The effective, one-electron hamiltonian is computed and compared to the corresponding uncorrelated, Hartree-Fock effective hamiltonian. Analysis of the functional suggests themore » need to construct different functionals for the same density and to allow a competition among these functions. As a result the correlation energy functional is composed explicitly of energy gaps from the different functionals.« less

Infrared spectroscopy of phenol-(H2O)(n>10): structural strains in hydrogen bond networks of neutral water clusters.

PubMed

Mizuse, Kenta; Hamashima, Toru; Fujii, Asuka

2009-11-05

To investigate hydrogen bond network structures of tens of water molecules, we report infrared spectra of moderately size (n)-selected phenol-(H2O)n (approximately 10 < or = n < or = approximately 50), which have essentially the same network structures as (H2O)(n+1). The phenyl group in phenol-(H2O)(n) allows us to apply photoionization-based size selection and infrared-ultraviolet double resonance spectroscopy. The spectra show a clear low-frequency shift of the free OH stretching band with increasing n. Detailed analyses with density functional theory calculations indicate that this shift is accounted for by the hydrogen bond network development from highly strained ones in the small (n < approximately 10) clusters to more relaxed ones in the larger clusters, in addition to the cooperativity of hydrogen bonds.

Role of intramolecular hydrogen bonding in the excited-state intramolecular double proton transfer (ESIDPT) of calix[4]arene: A TDDFT study

NASA Astrophysics Data System (ADS)

Wang, Se; Wang, Zhuang; Hao, Ce

2016-01-01

The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state intramolecular double proton transfer (ESIDPT) reaction of calix[4] arene (C4A) and the role of the intramolecular hydrogen bonds in the ESIDPT process. The geometries of C4A in the ground state and excited states (S1, S2 and T1) were optimized. Four intramolecular hydrogen bonds formed in the C4A are strengthened or weakened in the S2 and T1 states compared to those in the ground state. Interestingly, upon excitation to the S1 state of C4A, two protons H1 and H2 transfer along the two intramolecular hydrogen bonds O1-H1···O2 and O2-H2···O3, while the other two protons do not transfer. The ESIDPT reaction breaks the primary symmetry of C4A in the ground state. The potential energy curves of proton transfer demonstrate that the ESIDPT process follows the stepwise mechanism but not the concerted mechanism. Findings indicate that intramolecular hydrogen bonding is critical to the ESIDPT reactions in intramolecular hydrogen-bonded systems.

MD simulation study of the diffusion and local structure of n-alkanes in liquid and supercritical methanol at infinite dilution.

PubMed

Feng, Huajie; Gao, Wei; Su, Li; Sun, Zhenfan; Chen, Liuping

2017-06-01

The diffusion coefficients of 14 n-alkanes (ranging from methane to n-tetradecane) in liquid and supercritical methanol at infinite dilution (at a pressure of 10.5 MPa and at temperatures of 299 K and 515 K) were deduced via molecular dynamics simulations. Values for the radial distribution function, coordination number, and number of hydrogen bonds were then calculated to explore the local structure of each fluid. The flexibility of the n-alkane (as characterized by the computed dihedral distribution, end-to-end distance, and radius of gyration) was found to be a major influence and hydrogen bonding to be a minor influence on the local structure. Hydrogen bonding reduces the flexibility of the n-alkane, whereas increasing the temperature enhances its flexibility, with temperature having a greater effect than hydrogen bonding on flexibility. Graphical abstract The flexibility of the alkane is a major influence and the hydrogen bonding is a minor influence on the first solvation shell; the coordination numbers of long-chain n-alkanes in the first solvation shell are rather low.

Hydrogen bonding in water clusters and their ionized counterparts.

PubMed

Neela, Y Indra; Mahadevi, A Subha; Sastry, G Narahari

2010-12-30

Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H(2)O)(n), n = 2-20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts.

Tautomerism, molecular structure, intramolecular hydrogen bond, and enol-enol equilibrium of para halo substituted 4,4,4-trifluoro-1-phenyl-1,3-butanedione; Experimental and theoretical studies

NASA Astrophysics Data System (ADS)

Darugar, V. R.; Vakili, M.; Nekoei, A. R.; Tayyari, S. F.; Afzali, R.

2017-12-01

Para halo, X = F, Cl, and Br, substitution effect on tautomerism, keto-enol content, molecular structure, intramolecular hydrogen bonding, and enol-enol equilibrium constants of 4,4,4-trifluoro-1-phenyl-1,3-butanedione, known as trifluorobenzoylacetone (TFBA), have been investigated by means of density functional theory calculations and NMR, IR, and UV-Vis spectroscopic methods. Comparing the calculated and experimental results suggests coexisting of two stable cis-enol forms of titled molecules in comparable proportions in the sample. The theoretical and experimental results show that the equilibrium constants between both stable cis-enol forms of the studied molecules are similar, about 1.1-1.2. According to the AIM calculated results performed at the B3LYP/6-311++G∗∗ level, the target para halo molecules have a hydrogen bond strength of about 18.6 kcal/mol, as a medium hydrogen bond, similar to that of TFBA. The theoretical and experimental results indicate that there is no considerable difference between the hydrogen bond strength of the X-substituted titled molecules.

Temperature dependence of the evaporation lengthscale for water confined between two hydrophobic plates.

PubMed

Djikaev, Yuri S; Ruckenstein, Eli

2015-07-01

Liquid water in a hydrophobic confinement is the object of high interest in physicochemical sciences. Confined between two macroscopic hydrophobic surfaces, liquid water transforms into vapor if the distance between surfaces is smaller than a critical separation, referred to as the evaporation lengthscale. To investigate the temperature dependence of the evaporation lengthscale of water confined between two hydrophobic parallel plates, we use the combination of the density functional theory (DFT) with the probabilistic hydrogen bond (PHB) model for water-water hydrogen bonding. The PHB model provides an analytic expression for the average number of hydrogen bonds per water molecule as a function of its distance to a hydrophobic surface and its curvature. Knowing this expression, one can implement the effect of hydrogen bonding between water molecules on their interaction with the hydrophobe into DFT, which is then employed to determine the distribution of water molecules between two macroscopic hydrophobic plates at various interplate distances and various temperatures. For water confined between hydrophobic plates, our results suggest the evaporation lengthscale to be of the order of several nanometers and a linearly increasing function of temperature from T=293 K to T=333 K, qualitatively consistent with previous results. Copyright © 2015 Elsevier Inc. All rights reserved.

Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

PubMed

Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

2017-03-07

The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

Covalent functionalization of graphene by azobenzene with molecular hydrogen bonds for long-term solar thermal storage

NASA Astrophysics Data System (ADS)

Feng, Yiyu; Liu, Hongpo; Luo, Wen; Liu, Enzuo; Zhao, Naiqin; Yoshino, Katsumi; Feng, Wei

2013-11-01

Reduced graphene oxide-azobenzene (RGO-AZO) hybrids were prepared via covalent functionalization for long-term solar thermal storage. Thermal barrier (ΔEa) of cis to tran reversion and thermal storage (ΔH) were improved by molecular hydrogen bonds (H-bonds) through ortho- or para-substitution of AZO. Intramolecular H-bonds thermally stabilized cis-ortho-AZO on RGO with a long-term half-life of 5400 h (ΔEa = 1.2 eV), which was much longer than that of RGO-para-AZO (116 h). RGO-para-AZO with one intermolecular H-bond showed a high density of thermal storage up to 269.8 kJ kg-1 compared with RGO-ortho-AZO (149.6 kJ kg-1) with multiple intra- and intermolecular H-bonds of AZO according to relaxed stable structures. Thermal storage in experiment was the same order magnitude to theoretical data based on ΔH calculated by density functional theory and packing density. Photoactive RGO-AZO hybrid can be developed for high-performance solar thermal storage by optimizing molecular H-bonds.

Covalent functionalization of graphene by azobenzene with molecular hydrogen bonds for long-term solar thermal storage

PubMed Central

Feng, Yiyu; Liu, Hongpo; Luo, Wen; Liu, Enzuo; Zhao, Naiqin; Yoshino, Katsumi; Feng, Wei

2013-01-01

Reduced graphene oxide-azobenzene (RGO-AZO) hybrids were prepared via covalent functionalization for long-term solar thermal storage. Thermal barrier (ΔEa) of cis to tran reversion and thermal storage (ΔH) were improved by molecular hydrogen bonds (H-bonds) through ortho- or para-substitution of AZO. Intramolecular H-bonds thermally stabilized cis-ortho-AZO on RGO with a long-term half-life of 5400 h (ΔEa = 1.2 eV), which was much longer than that of RGO-para-AZO (116 h). RGO-para-AZO with one intermolecular H-bond showed a high density of thermal storage up to 269.8 kJ kg−1 compared with RGO-ortho-AZO (149.6 kJ kg−1) with multiple intra- and intermolecular H-bonds of AZO according to relaxed stable structures. Thermal storage in experiment was the same order magnitude to theoretical data based on ΔH calculated by density functional theory and packing density. Photoactive RGO-AZO hybrid can be developed for high-performance solar thermal storage by optimizing molecular H-bonds. PMID:24247355

Covalent functionalization of graphene by azobenzene with molecular hydrogen bonds for long-term solar thermal storage.

PubMed

Feng, Yiyu; Liu, Hongpo; Luo, Wen; Liu, Enzuo; Zhao, Naiqin; Yoshino, Katsumi; Feng, Wei

2013-11-19

Reduced graphene oxide-azobenzene (RGO-AZO) hybrids were prepared via covalent functionalization for long-term solar thermal storage. Thermal barrier (ΔEa) of cis to tran reversion and thermal storage (ΔH) were improved by molecular hydrogen bonds (H-bonds) through ortho- or para-substitution of AZO. Intramolecular H-bonds thermally stabilized cis-ortho-AZO on RGO with a long-term half-life of 5400 h (ΔEa = 1.2 eV), which was much longer than that of RGO-para-AZO (116 h). RGO-para-AZO with one intermolecular H-bond showed a high density of thermal storage up to 269.8 kJ kg(-1) compared with RGO-ortho-AZO (149.6 kJ kg(-1)) with multiple intra- and intermolecular H-bonds of AZO according to relaxed stable structures. Thermal storage in experiment was the same order magnitude to theoretical data based on ΔH calculated by density functional theory and packing density. Photoactive RGO-AZO hybrid can be developed for high-performance solar thermal storage by optimizing molecular H-bonds.

Infrared signature of micro-hydration in the organophosphate sarin: An ab initio study

DOE PAGES

Alam, Todd M.; Pearce, Charles Joseph

2015-06-28

The infrared (IR) spectra of micro-hydrated Sarin•(H 2O) n clusters containing between one and four explicit waters have been studied using ab initio density functional theory (DFT) methods. The phosphate group P=O bond vibration region (~1270 to 1290 cm –1) revealed the largest frequency variation with hydration, with a frequency red shift reflecting the direct hydrogen bond formation between the P=O of Sarin and water. Small variations to the P-F stretch (~810 to 815 cm –1) and the C-O-P vibrational modes (~995 to 1004 cm –1) showed that the water interactions with these functional groups were minor, and that themore » structures of Sarin were not extensively perturbed in the hydrated complexes. Increasing the number of explicit hydration waters produced only small vibrational changes in the lowest free energy complexes. These minor changes were consistent with a single water-phosphate hydrogen bond being the dominant structure, though a second water-phosphate hydrogen bond was observed in some complexes and was identified by an additional red shift of the P=O bond vibration. As a result, the H 2O•H 2O vibrational modes (~3450 to 3660 cm –1) increased in complexity with higher hydration levels and reflect the extended hydrogen bonding networks formed between the explicit waters in the hydrated Sarin clusters.« less

Insight into Environmental Effects on Bonding and Redox Properties of [4Fe-4S] Clusters in Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niu, Shuqiang; Ichiye, Toshiko

The large differences in redox potentials between the HiPIPs and ferredoxins are generally attributed to hydrogen bonds and electrostatic effects from the protein and solvent. Recent ligand K-edge X-ray absorption studies by Solomon and co-workers show that the Fe-S covalencies of [4Fe-4S] clusters in the two proteins differ considerably apparently because of hydrogen bonds from water, indicating electronic effects may be important. However, combined density function theory (DFT) and photoelectron spectroscopy studies by our group and Wang and co-workers indicate that hydrogen bonds tune the potential of [4Fe-4S] clusters by mainly electrostatics. The DFT studies here rationalize both results, namelymore » that the observed change in the Fe-S covalency is due to differences in ligand conformation between the two proteins rather than hydrogen bonds. Moreover, the ligand conformation affects the calculated potentials by 100 mV and, thus, is a heretofore unconsidered means of tuning the potential.« less

Unexpected regioselective carbon-hydrogen bond activation/cyclization of indolyl aldehydes or ketones with alkynes to benzo-fused oxindoles.

PubMed

Liu, Xingyan; Li, Gaocan; Song, Feijie; You, Jingsong

2014-09-25

Rhodium-catalyzed carbon-hydrogen bond activation has attracted great interest in the construction of carbon-carbon and carbon-heteroatom bonds. In recent years, transition metal-mediated oxygen transposition through a 'dehydration-rehydration' process has been considered as a promising strategy towards oxygen-functionalized compounds. Here we describe an unexpected rhodium-catalyzed regioselective carbon-hydrogen bond activation/cyclization of easily available indolyl aldehydes or ketones with alkynes to afford benzo-fused oxindoles, involving the sequential carbonyl-assisted carbon-hydrogen activation of the indole ring at the 4-position, [4+2] cyclization, aromatization via dehydration, nucleophilic addition of water to iminium and oxidation. Isotopic labelling experiments disclose the occurrence of apparent oxygen transposition via dehydration-rehydration from the indolyl-3-carbonyl group to the 2-position of pyrrole to forge a new carbonyl bond. The tandem reaction has been used as the key step for the concise synthesis of priolines, a type of alkaloid isolated from the roots of Salvia prionitis.

Hydrogen Bond Lifetimes and Energetics for Solute-Solvent Complexes Studied with 2D-IR Vibrational Echo Spectroscopy

PubMed Central

Zheng, Junrong; Fayer, Michael D.

2008-01-01

Weak π hydrogen bonded solute-solvent complexes are studied with ultrafast two dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy, temperature dependent IR absorption spectroscopy, and density functional theory calculations. Eight solute-solvent complexes composed of a number of phenol derivatives and various benzene derivatives are investigated. The complexes are formed between the phenol derivative (solute) in a mixed solvent of the benzene derivative and CCl4. The time dependence of the 2D-IR vibrational echo spectra of the phenol hydroxyl stretch is used to directly determine the dissociation and formation rates of the hydrogen bonded complexes. The dissociation rates of the weak hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. The results are discussed in terms of transition state theory. PMID:17373792

Water's hydrogen bonds in the hydrophobic effect: a simple model.

PubMed

Xu, Huafeng; Dill, Ken A

2005-12-15

We propose a simple analytical model to account for water's hydrogen bonds in the hydrophobic effect. It is based on computing a mean-field partition function for a water molecule in the first solvation shell around a solute molecule. The model treats the orientational restrictions from hydrogen bonding, and utilizes quantities that can be obtained from bulk water simulations. We illustrate the principles in a 2-dimensional Mercedes-Benz-like model. Our model gives good predictions for the heat capacity of hydrophobic solvation, reproduces the solvation energies and entropies at different temperatures with only one fitting parameter, and accounts for the solute size dependence of the hydrophobic effect. Our model supports the view that water's hydrogen bonding propensity determines the temperature dependence of the hydrophobic effect. It explains the puzzling experimental observation that dissolving a nonpolar solute in hot water has positive entropy.

Selective C70 encapsulation by a robust octameric nanospheroid held together by 48 cooperative hydrogen bonds

PubMed Central

Markiewicz, Grzegorz; Jenczak, Anna; Kołodziejski, Michał; Holstein, Julian J.; Stefankiewicz, Artur R

2017-01-01

Self-assembly of multiple building blocks via hydrogen bonds into well-defined nanoconstructs with selective binding function remains one of the foremost challenges in supramolecular chemistry. Here, we report the discovery of a enantiopure nanocapsule that is formed through the self-assembly of eight amino acid functionalised molecules in nonpolar solvents through 48 hydrogen bonds. The nanocapsule is remarkably robust, being stable at low and high temperatures, and in the presence of base, presumably due to the co-operative geometry of the hydrogen bonding motif. Thanks to small pore sizes, large internal cavity and sufficient dynamicity, the nanocapsule is able to recognize and encapsulate large aromatic guests such as fullerenes C60 and C70. The structural and electronic complementary between the host and C70 leads to its preferential and selective binding from a mixture of C60 and C70. PMID:28488697

Multiple hydrogen-bonded complexes based on 2-ureido-4[1H]-pyrimidinone: a theoretical study.

PubMed

Sun, Hao; Lee, Hui Hui; Blakey, Idriss; Dargaville, Bronwin; Chirila, Traian V; Whittaker, Andrew K; Smith, Sean C

2011-09-29

In the present work, the electronic structures and properties of a series of 2-ureido-4[1H]-pyrimidinone(UPy)-based monomers and dimers in various environments (vacuum, chloroform, and water) are studied by density functional theoretical methods. Most dimers prefer to form a DDAA-AADD (D, H-bond donor; A, H-bond acceptor) array in both vacuum and solvents. Topological analysis proved that intramolecular and intermolecular hydrogen bonds coexist in the dimers. Frequency and NBO calculations show that all the hydrogen bonds exhibit an obvious red shift in their stretching vibrational frequencies. Larger substituents at position 6 of the pyrimidinone ring with stronger electron-donating ability favor the total binding energy and free energy of dimerization. Calculations on the solvent effect show that dimerization is discouraged by the stronger polarity of the solvent. Further computations show that Dimer-1 may be formed in chloroform, but water molecules may interact with the donor or acceptor sites and hence disrupt the hydrogen bonds of Dimer-1. © 2011 American Chemical Society

Two-dimensional infrared spectroscopy of intermolecular hydrogen bonds in the condensed phase.

PubMed

Elsaesser, Thomas

2009-09-15

Hydrogen bonding plays a key role in the structural, physical, and chemical properties of liquids such as water and in macromolecular structures such as proteins. Vibrational spectroscopy is an important tool for understanding hydrogen bonding because it provides a way to observe local molecular geometries and their interaction with the environment. Linear vibrational spectroscopy has mapped characteristic changes of vibrational spectra and the occurrence of new bands that form upon hydrogen bonding. However, linear vibrational spectroscopy gives very limited insight into ultrafast dynamics of the underlying molecular interactions, such as the motions of hydrogen-bonded groups, energy dissipation and delocalization, and the fluctuations within hydrogen-bonded structures that occur in the ultrafast time domain. Nonlinear vibrational spectroscopy with its femtosecond time resolution can discern these dynamic processes in real time and has emerged as an important tool for unraveling molecular dynamics and for quantifying interactions that govern the vibrational and structural dynamics of hydrogen bonds. This Account reviews recent progress originating from third-order nonlinear methods of coherent multidimensional vibrational spectroscopy. Ultrafast dynamics of intermolecular hydrogen bonds are addressed for a number of prototype systems: hydrogen-bonded carboxylic acid dimers in an aprotic liquid environment, the disordered fluctuating hydrogen-bond network of liquid water, and DNA oligomers interacting with water. Cyclic carboxylic acid dimers display a rich scheme of vibrational couplings, resulting in OH stretching absorption bands with highly complex spectral envelopes. Two-dimensional spectroscopy of acetic acid dimers in a nonpolar liquid environment demonstrates that multiple Fermi resonances of the OH stretching mode with overtones and combination tones of fingerprint vibrations dominate both the 2D and linear absorption spectra. The coupling of the OH stretching mode with low-frequency hydrogen-bonding modes leads to additional progressions and coherent low-frequency hydrogen-bond motions in the subpicosecond time domain. In water, the 2D spectra reveal ultrafast spectral diffusion on a sub-100 fs time scale caused by the ultrafast structural fluctuations of the strongly coupled hydrogen-bond network. Librational motions play a key role for the ultrafast loss of structural memory. Spectral diffusion rates are enhanced by resonant transfer of OH stretching quanta between water molecules, typically occurring on a 100 fs time scale. In DNA oligomers, femtosecond nonlinear vibrational spectroscopy resolves NH and OH stretching bands in the highly congested infrared spectra of these molecules, which contain alternating adenine-thymine pairs. Studies at different levels of hydration reveal the spectral signatures of water molecules directly interacting with the phosphate groups of DNA and of a second water species forming a fluctuating environment around the DNA oligomers. We expect that the application of 2D infrared spectroscopy in an extended spectral range will reveal the intrinsic coupling between water and specific functional units of DNA.

Complementary Strategies for Directed C(sp3 )-H Functionalization: A Comparison of Transition-Metal-Catalyzed Activation, Hydrogen Atom Transfer, and Carbene/Nitrene Transfer.

PubMed

Chu, John C K; Rovis, Tomislav

2018-01-02

The functionalization of C(sp 3 )-H bonds streamlines chemical synthesis by allowing the use of simple molecules and providing novel synthetic disconnections. Intensive recent efforts in the development of new reactions based on C-H functionalization have led to its wider adoption across a range of research areas. This Review discusses the strengths and weaknesses of three main approaches: transition-metal-catalyzed C-H activation, 1,n-hydrogen atom transfer, and transition-metal-catalyzed carbene/nitrene transfer, for the directed functionalization of unactivated C(sp 3 )-H bonds. For each strategy, the scope, the reactivity of different C-H bonds, the position of the reacting C-H bonds relative to the directing group, and stereochemical outcomes are illustrated with examples in the literature. The aim of this Review is to provide guidance for the use of C-H functionalization reactions and inspire future research in this area. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Study on the choice of functional monomer before preparation of myclobutanil molecularly imprinted polymer].

PubMed

Gao, Wen-Hui; Liu, Bo; Li, Xing-Feng; Han, Jun-Hua; Jia, Ying-Min

2014-03-01

To prepare myclobutanil molecularly imprinted polymer, a method was established for the choice of the appropriate functional monomer and its dosage. UV spectra was applied to study the combination form, the effect intensity, the optimal concentration ratio and the numbers of binding sites between myclobutanil and methyl acrylic acid (MAA) or acrylamide (AM) functional monomer. The results showed that hydrogen-bonding interaction could be formed between myclobutanil and methyl acrylic acid (MAA) or acrylamide (AM) functional monomer. The pi electron of the triazole ring conjugated double bond in my clobutanil could transit to pi* conjugate antibonding orbital when it absorbed energy. The formation of hydrogen bond could make pi-->pi* absorption band transit. Maximum absorption wavelength produced red shift with the increase in the functional monomer concentration in the system. The research revealed that the optimal concentration ratios between myclobutanil and the two monomers were c(M):c(MAA) = 1:4, c(M):c(AM) = 1:2. Myclobutanil and the both the functional monomers had the bonding ability, and strong bonding force. The prepared molecularly imprinted polymer using AM as a functional monomer had better stability and specificity of recognition for myclobutanil.

Protonic transport through solitons in hydrogen-bonded systems

NASA Astrophysics Data System (ADS)

Kavitha, L.; Jayanthi, S.; Muniyappan, A.; Gopi, D.

2011-09-01

We offer an alternative route for investigating soliton solutions in hydrogen-bonded (HB) chains. We invoke the modified extended tangent hyperbolic function method coupled with symbolic computation to solve the governing equation of motion for proton dynamics. We investigate the dynamics of proton transfer in HB chains through bell-shaped soliton excitations, which trigger the bio-energy transport in most biological systems. This solitonic mechanism of proton transfer could play functional roles in muscular contraction, enzymatic activity and oxidative phosphorylation.

Chromatographic Assessment of Hydrogen-Bond Donating Ability

DTIC Science & Technology

1993-04-22

hydrogen-bond donors used in cocrystallizations . Hydrogen-bond donor solutes are chromatographed on a poly(vinylpyridine-divinylbenzene) column under...provides an a priori measure of the hydrogen- bond acidity of a potential cocrystal component. 20 DISTRIBUTION /AVAILABILITY OF ABSTRACT 21 ABSTRACT...general heuristic principle that has guided our cocrystallization studies is "the best hydrogen-bond donor hydrogen bonds to the best hydrogen-bond acceptor

Single crystal, vibrational and computational studies of Theophylline (a bronchodilator drug) and its chloride salt

NASA Astrophysics Data System (ADS)

Mary Novena, L.; Suresh Kumar, S.; Athimoolam, S.; Saminathan, K.; Sridhar, B.

2017-04-01

The crystal structure of Theophylline (TH) and Theophyillinium chloride monohydrate (THC) and its complete molecular structure analysis on theoretical and experimental methods is reported here. The hydrogen bonding studies were carried out as a special note of the present work. The electron density analyses of the compounds were also analyzed in view of the intermolecular interactions. Moreover, it is an ever first quantum chemical report of this drug (TH) and its chloride salt. In TH crystal, the water molecule connects the Theophylline molecules through Osbnd H⋯N hydrogen bond forming discrete D22(7) motif and dimeric ring R22(10) motif through Nsbnd H⋯O hydrogen bond. In THC, the two classical (Nsbnd H⋯O, Nsbnd H⋯Cl) and one non-classical (Csbnd H⋯O) hydrogen bonds produce two pentameric chain C55 (16) and C55(17) motifs. These two chain motifs are interconnected by Osbnd H⋯O hydrogen bond and cross linked by Nsbnd H⋯Cl and Osbnd H⋯Cl hydrogen bonds to produce octametric ring R88(27) and R88(28) motifs. The solubility test is carried out to enhance the drug solubility and the therapeutic effectiveness of the drug. Experimentally obtained vibrational wavenumbers are compared with the spectra obtained theoretically for both the compound. The strong intensity bands and the shifting of bands due to intermolecular hydrogen bonds are also investigated. The Mulliken atomic charges, HOMO-LUMO and thermodynamic properties are calculated using Density Functional Theory (DFT) and Hartree-Fock Theory (HF) using 6-311++G(d,p) basis set.

Activation and thermodynamic parameter study of the heteronuclear C=O···H-N hydrogen bonding of diphenylurethane isomeric structures by FT-IR spectroscopy using the regularized inversion of an eigenvalue problem.

PubMed

Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro

2012-08-02

The doublet of the ν(C=O) carbonyl band in isomeric urethane systems has been extensively discussed in qualitative terms on the basis of FT-IR spectroscopy of the macromolecular structures. Recently, a reaction extent model was proposed as an inverse kinetic problem for the synthesis of diphenylurethane for which hydrogen-bonded and non-hydrogen-bonded C=O functionalities were identified. In this article, the heteronuclear C=O···H-N hydrogen bonding in the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol was investigated via FT-IR spectroscopy, using a methodology of regularization for the inverse reaction extent model through an eigenvalue problem. The kinetic and thermodynamic parameters of this system were derived directly from the spectroscopic data. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied. The study determined the enthalpy (ΔH = 15.25 kJ/mol), entropy (TΔS = 14.61 kJ/mol), and free energy (ΔG = 0.6 kJ/mol) of heteronuclear C=O···H-N hydrogen bonding by FT-IR spectroscopy through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S, and δΔ(‡)G) at equilibrium in the chemical reaction system. The parameters obtained in this study may contribute toward a better understanding of the properties of, and interactions in, supramolecular systems, such as the switching behavior of hydrogen bonding.

Orientation hydrogen-bonding effect on vibronic spectra of isoquinoline in water solvent: Franck-Condon simulation and interpretation

NASA Astrophysics Data System (ADS)

Liu, Yu-Hui; Wang, Shi-Ming; Wang, Chen-Wen; Zhu, Chaoyuan; Han, Ke-Li; Lin, Sheng-Hsien

2016-10-01

The excited-state orientation hydrogen-bonding dynamics, and vibronic spectra of isoquinoline (IQ) and its cationic form IQc in water have been investigated at the time-dependent density functional theory quantum chemistry level plus Franck-Condon simulation and interpretation. The excited-state orientation hydrogen bond strengthening has been found in IQ:H2O complex due to the charge redistribution upon excitation; this is interpreted by simulated 1:1 mixed absorption spectra of free IQ and IQ:H2O complex having best agreement with experimental results. Conversely, the orientation hydrogen bond in IQc:H2O complex would be strongly weakening in the S1 state and this is interpreted by simulated absorption spectra of free IQc having best agreement with experimental results. By performing Franck-Condon simulation, it reveals that several important vibrational normal modes with frequencies about 1250 cm-1 involving the wagging motion of the hydrogen atoms are very sensitive to the formation of the orientation hydrogen bond for the IQ/IQc:H2O complex and this is confirmed by damped Franck-Condon simulation with free IQ/IQc in water. However, the emission spectra of the IQ and IQc in water have been found differently. Upon the excitation, the simulated fluorescence of IQ in water is dominated by the IQ:H2O complex; thus hydrogen bond between IQ and H2O is much easier to form in the S1 state. While the weakened hydrogen bond in IQc:H2O complex is probably cleaved upon the laser pulse because the simulated emission spectrum of the free IQc is in better agreement with the experimental results.

Ruthenium-catalyzed insertion of adjacent diol carbon atoms into C-C bonds: Entry to type II polyketides.

PubMed

Bender, Matthias; Turnbull, Ben W H; Ambler, Brett R; Krische, Michael J

2017-08-25

Current catalytic processes involving carbon-carbon bond activation rely on π-unsaturated coupling partners. Exploiting the concept of transfer hydrogenative coupling, we report a ruthenium(0)-catalyzed cycloaddition of benzocyclobutenones that functionalizes two adjacent saturated diol carbon-hydrogen bonds. These regio- and diastereoselective processes enable convergent construction of type II polyketide substructures. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Hydrogen bonds in concreto and in computro: the sequel

NASA Astrophysics Data System (ADS)

Stouten, Pieter F. W.; Van Eijck, Bouke P.; Kroon, Jan

1991-02-01

In the framework of our comparative research concerning hydrogen bonding in the crystalline and liquid phases we have carried out molecular dynamics (MD) simulations of liquid methanol. Six different rigid three site models are compared. Five of them had been reported in the literature and one (OM2) we developed by a fit to the experimental molar volume, heat of vaporization and neutron weighted radial distribution function. In general the agreement with experiment is satisfactory for the different models. None of the models has an explicit hydrogen bond potential, but five of the six models show a degree of hydrogen bonding comparable to experiments on liquid methanol. The analysis of the simulation hydrogen bonds indicates that there is a distinct preference of the O⋯O axis to lie in the acceptor lone pairs plane, but hardly any for the lone pair directions. Ab initio calculations and crystal structure statistics of OH⋯O hydrogen bonds agree with this observation. The O⋯O hydrogen bond length distributions are similar for most models. The crystal structures show a sharper O⋯O distribution. Explicit introduction of harmonic motion with a quite realistic root mean square amplitude of 0.08 Å to the thermally averaged crystal distribution results in a distribution comparable to OM2 although the maximum of the former is found at shorter distance. On the basis of the analysis of the static properties of all models we conclude that our OM2, Jorgenson's OPLS and Haughney, Ferrario and McDonald's HFM1 models are good candidates for simulations of liquid methanol under isothermal, isochoric conditions. Partly flexible and completely rigid OM2 are simulated at constant pressure and with fixed volume. The flexible simulations give essentially the same (correct) results under both conditions, which is not surprising because the flexible form was fitted under both conditions. Rigid OM2 has a similar potential energy but larger pressure in the isochoric case and larger energy and far larger volume in the isobaric case. Radial distribution functions and hydrogen bond geometries are very similar for all four cases. Only in the case of the osobaric rigid methanol does the volume expansion seem to be accompanied by a slight preference for tetrahedrality around the oxygen atom.

Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.

PubMed

Horowitz, Scott; Dirk, Lynnette M A; Yesselman, Joseph D; Nimtz, Jennifer S; Adhikari, Upendra; Mehl, Ryan A; Scheiner, Steve; Houtz, Robert L; Al-Hashimi, Hashim M; Trievel, Raymond C

2013-10-16

S-adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon-oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.

Anharmonic calculations of frequencies and intensities of Osbnd H stretching vibrations of (R)-1,3-butanediol conformers in the fundamentals and first overtones by density functional theory

NASA Astrophysics Data System (ADS)

Futami, Yoshisuke; Minamoto, Chihiro; Kudoh, Satoshi

2018-05-01

The frequencies and absorption intensities of the five kinds of conformers of 1,3-butanediol with the same carbon skeleton (GG‧) were calculated by anharmonic calculation for the fundamentals and first overtones of OH stretching vibrations. The four kinds of conformers form intramolecular hydrogen bonds and one conformer did not. Intramolecular hydrogen bond formation shifted the frequency of fundamental and first overtone of H-bonding OH stretching vibration to the lower frequency. The absorption intensities of the fundamentals as well as the vibrational anharmonicities increased upon hydrogen bond formation, while the intensities of first overtones decreased. The differences of conformers were clearly seen in the frequencies of the first overtones of free OH.

Spectroscopic investigation on cocrystal formation between adenine and fumaric acid based on infrared and Raman techniques

NASA Astrophysics Data System (ADS)

Du, Yong; Fang, Hong Xia; Zhang, Qi; Zhang, Hui Li; Hong, Zhi

2016-01-01

As an important component of double-stranded DNA, adenine has powerful hydrogen-bond capability, due to rich hydrogen bond donors and acceptors existing within its molecular structure. Therefore, it is easy to form cocrystal between adenine and other small molecules with intermolecular hydrogen-bond effect. In this work, cocrystal of adenine and fumaric acid has been characterized as model system by FT-IR and FT-Raman spectral techniques. The experimental results show that the cocrystal formed between adenine and fumaric acid possesses unique spectroscopical characteristic compared with that of starting materials. Density functional theory (DFT) calculation has been performed to optimize the molecular structures and simulate vibrational modes of adenine, fumaric acid and the corresponding cocrystal. Combining the theoretical and experimental vibrational results, the characteristic bands corresponding to bending and stretching vibrations of amino and carbonyl groups within cocrystal are shifted into lower frequencies upon cocrystal formation, and the corresponding bond lengths show some increase due to the effect of intermolecular hydrogen bonding. Different vibrational modes shown in the experimental spectra have been assigned based on the simulation DFT results. The study could provide experimental and theoretical benchmarks to characterize cocrystal formed between active ingredients and cocrystal formers and also the intermolecular hydrogen-bond effect within cocrystal formation process by vibrational spectroscopic techniques.

Polymer blend compositions and methods of preparation

DOEpatents

Naskar, Amit K.

2016-09-27

A polymer blend material comprising: (i) a first polymer containing hydrogen bond donating groups having at least one hydrogen atom bound to a heteroatom selected from oxygen, nitrogen, and sulfur, or an anionic version of said first polymer wherein at least a portion of hydrogen atoms bound to a heteroatom is absent and replaced with at least one electron pair; (ii) a second polymer containing hydrogen bond accepting groups selected from nitrile, halogen, and ether functional groups; and (iii) at least one modifying agent selected from carbon particles, ether-containing polymers, and Lewis acid compounds; wherein, if said second polymer contains ether functional groups, then said at least one modifying agent is selected from carbon particles and Lewis acid compounds. Methods for producing the polymer blend, molded forms thereof, and articles thereof, are also described.

Quantitative estimation of pesticide-likeness for agrochemical discovery.

PubMed

Avram, Sorin; Funar-Timofei, Simona; Borota, Ana; Chennamaneni, Sridhar Rao; Manchala, Anil Kumar; Muresan, Sorel

2014-12-01

The design of chemical libraries, an early step in agrochemical discovery programs, is frequently addressed by means of qualitative physicochemical and/or topological rule-based methods. The aim of this study is to develop quantitative estimates of herbicide- (QEH), insecticide- (QEI), fungicide- (QEF), and, finally, pesticide-likeness (QEP). In the assessment of these definitions, we relied on the concept of desirability functions. We found a simple function, shared by the three classes of pesticides, parameterized particularly, for six, easy to compute, independent and interpretable, molecular properties: molecular weight, logP, number of hydrogen bond acceptors, number of hydrogen bond donors, number of rotatable bounds and number of aromatic rings. Subsequently, we describe the scoring of each pesticide class by the corresponding quantitative estimate. In a comparative study, we assessed the performance of the scoring functions using extensive datasets of patented pesticides. The hereby-established quantitative assessment has the ability to rank compounds whether they fail well-established pesticide-likeness rules or not, and offer an efficient way to prioritize (class-specific) pesticides. These findings are valuable for the efficient estimation of pesticide-likeness of vast chemical libraries in the field of agrochemical discovery. Graphical AbstractQuantitative models for pesticide-likeness were derived using the concept of desirability functions parameterized for six, easy to compute, independent and interpretable, molecular properties: molecular weight, logP, number of hydrogen bond acceptors, number of hydrogen bond donors, number of rotatable bounds and number of aromatic rings.

Neural Plasticity and Memory: Is Memory Encoded in Hydrogen Bonding Patterns?

PubMed

Amtul, Zareen; Rahman, Atta-Ur

2016-02-01

Current models of memory storage recognize posttranslational modification vital for short-term and mRNA translation for long-lasting information storage. However, at the molecular level things are quite vague. A comprehensive review of the molecular basis of short and long-lasting synaptic plasticity literature leads us to propose that the hydrogen bonding pattern at the molecular level may be a permissive, vital step of memory storage. Therefore, we propose that the pattern of hydrogen bonding network of biomolecules (glycoproteins and/or DNA template, for instance) at the synapse is the critical edifying mechanism essential for short- and long-term memories. A novel aspect of this model is that nonrandom impulsive (or unplanned) synaptic activity functions as a synchronized positive-feedback rehearsal mechanism by revising the configurations of the hydrogen bonding network by tweaking the earlier tailored hydrogen bonds. This process may also maintain the elasticity of the related synapses involved in memory storage, a characteristic needed for such networks to alter intricacy and revise endlessly. The primary purpose of this review is to stimulate the efforts to elaborate the mechanism of neuronal connectivity both at molecular and chemical levels. © The Author(s) 2014.

Mechanistic Insights on the Hydrogenation of α,β-Unsaturated Ketones and Aldehydes to Unsaturated Alcohols over Metal Catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ide, Matthew S.; Hao, Bing; Neurock, Matthew

The selective hydrogenation of unsaturated ketones (methyl vinyl ketone and benzalacetone) and unsaturated aldehydes (crotonaldehyde and cinnamaldehyde) was carried out with H₂ at 2 bar absolute over Pd/C, Pt/C, Ru/C, Au/C, Au/TiO₂, or Au/Fe₂O₃ catalysts in ethanol or water solvent at 333 K. Comparison of the turnover frequencies revealed Pd/C to be the most active hydrogenation catalyst, but the catalyst failed to produce unsaturated alcohols, indicating hydrogenation of the C=C bond was highly preferred over the C=O bond on Pd. The Pt and Ru catalysts were able to produce unsaturated alcohols from unsaturated aldehydes, but not from unsaturated ketones. Althoughmore » Au/ Fe₂O₃ was able to partially hydrogenate unsaturated ketones to unsaturated alcohols, the overall hydrogenation rate over gold was the lowest of all of the metals examined. First-principles density functional theory calculations were therefore used to explore the reactivity trends of methyl vinyl ketone (MVK) and benzalacetone (BA) hydrogenation over model Pt(111) and Ru(0001) surfaces. The observed selectivity over these metals is likely controlled by the significantly higher activation barriers to hydrogenate the C=O bond compared with those required to hydrogenate the C=C bond. Both the unsaturated alcohol and the saturated ketone, which are the primary reaction products, are strongly bound to Ru and can react further to the saturated alcohol. The lower calculated barriers for the hydrogenation steps over Pt compared with Ru account for the higher observed turnover frequencies for the hydrogenation of MVK and BA over Pt. The presence of a phenyl substituent α to the C=C bond in BA increased the barrier for C=C hydrogenation over those associated with the C=C bond in MVK; however, the increase in barriers with phenyl substitution was not adequate to reverse the selectivity trend.« less

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

PubMed Central

Wolters, Lando P; Bickelhaupt, F Matthias

2012-01-01

We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A− and the analogous hydrogen-bonded complexes DH⋅⋅⋅A− (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn–Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A− arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO–LUMO interactions between the lone pair of A− and the σ* orbital of D–X. PMID:24551497

Molecular Dynamics Study of the Proposed Proton Transport Pathways in [FeFe]-Hydrogenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.

2014-01-15

Possible proton channels in Clostridium pasteurianum [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to discern proposed channels, compare their properties, evaluate the functional channel, and to provide insight into the features of an active proton channel. Our simulations suggest that protons are not transported through water wires. Instead, a five-residue motif (E282, S319, E279, HOH, C299) was found to be the likely channel, consistent with experimental observations. This channel connects the surface of the enzyme and the di-thiomethylamine bridge of the catalytic H-cluster, permitting the transport of protons. The channel was found to have a persistentmore » hydrogen bonded core (residues E279 to S319), with less persistent hydrogen bonds at the ends of the channel. The hydrogen bond occupancy in this network was found to be sensitive to the protonation state of the residues in the channel, with different protonation states enhancing or stabilizing hydrogen bonding in different regions of the network. Single site mutations to non-hydrogen bonding residues break the hydrogen bonding network at that residue, consistent with experimental observations showing catalyst inactivation. In many cases, these mutations alter the hydrogen bonding in other regions of the channel which may be equally important in catalytic failure. A correlation between the protein dynamics near the proton channel and the redox partner binding regions was also found as a function of protonation state. The likely mechanism of proton movement in [FeFe]-hydrogenases is discussed based on the structural analysis presented here. This work was funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory, and a portion of the research was performed using PNNL Institutional Computing at Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Chemical Constraints Governing the Origin of Metabolism: The Thermodynamic Landscape of Carbon Group Transformations

NASA Technical Reports Server (NTRS)

Weber, Arthur L.; Fonda, Mark (Technical Monitor)

2001-01-01

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies were estimated for four types reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed that (1) when carbon-carbon bond cleavage involves two different types of functional groups, transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) the energy of carbon-carbon bond transformation is strongly dependent on the type of functional group that donates the shared electron-pair during cleavage, and the group that accepts the shared electron-pair during synthesis, and (3) the energetics of C-C bond transformation is determined primarily by the half-reaction energies of the couples: carbonyl/carboxylic acid, carboxylic acid/carbon dioxide, alcohol/carbonyl, and hydrocarbon/alcohol. The energy of hydrogen-transfer between carbon groups was found to depend on the functional group class of both the hydrogen-donor and hydrogen-acceptor. From these and other observations we concluded that the chemistry of the origin of metabolism (and to a lesser degree modem metabolism) is strongly constrained by the (1) limited disproportionation energy of organic substrates that can be dissipated in a few irreversible reactions, (2) the energy-dominance of few half-reaction couples in carbon-carbon bond transformation that establishes whether a chemical reaction is energetically irreversible, reversible or unfeasible, and (3) the dependence of the transformation-energy on the oxidation state of carbon groups (functional group type) which is contingent on prior reactions in the synthetic pathway.

Synthesis and characterization of hydrogen-bond acidic functionalized graphene

NASA Astrophysics Data System (ADS)

Yang, Liu; Han, Qiang; Pan, Yong; Cao, Shuya; Ding, Mingyu

2014-05-01

Hexafluoroisopropanol phenyl group functionalized materials have great potential in the application of gas-sensitive materials for nerve agent detection, due to the formation of strong hydrogen-bonding interactions between the group and the analytes. In this paper, take full advantage of ultra-large specific surface area and plenty of carbon-carbon double bonds and hexafluoroisopropanol phenyl functionalized graphene was synthesized through in situ diazonium reaction between -C=C- and p-hexafluoroisopropanol aniline. The identity of the as-synthesis material was confirmed by transmission electron microscopy, Raman spectroscopy, ultraviolet visible spectroscopy, X-ray photoelectron spectroscopy and thermo gravimetric analysis. The synthesis method is simply which retained the excellent physical properties of original graphene. In addition, the novel material can be assigned as an potential candidate for gas sensitive materials towards organophosphorus nerve agent detection.

Direct atomic force microscopic evidence of hydrogen bonding interaction in phosphatidic acid Langmuir-Blodgett bilayer

NASA Astrophysics Data System (ADS)

Chunbo, Yuan; Ying, Wu; Yueming, Sun; Zuhong, Lu; Juzheng, Liu

1997-12-01

Molecularly resolved atomic force microscopic images of phosphatidic acid Langmuir-Blodgett bilayers show that phosphate groups in polar region of the films are packing in a distorted hexagonal organization with long-range orientational and positional order. Intermolecular hydrogen bonding interactions, which should be responsible for the ordering and stability of bilayers, are visualized directly between adjacent phosphate groups in the polar region of the bilayer. Some adjacent phosphatidic acid molecules link each other through the formation of intermolecular hydrogen bonds between phosphate groups in polar region to form local supramolecules, which provide the bilayer's potential as a functionized film in the investigation on the lateral conductions of protons in the biological bilayers.

A DFT investigation on interactions between asymmetric derivatives of cisplatin and nucleobase guanine

NASA Astrophysics Data System (ADS)

Tai, Truong Ba; Nhat, Pham Vu

2017-07-01

The interactions of hydrolysis products of cisplatin and its asymmetric derivatives cis- and trans-[PtCl2(iPram)(Mepz)] with guanine were studied using DFT methods. These interactions are dominated by electrostatic effects, namely hydrogen bond contributions and there exists a charge flow from H-atoms of ligands to the O-atoms of guanine. The replacement of NH3 moieties by larger functional groups accompanies with a moderate reaction between PtII and guanine molecule, diminishing the cytotoxicity of the drug. The asymmetric and symmetric NH2 stretching modes of complexes having strong hydrogen bond interactions are red shifted importantly as compared to complexes without presence of hydrogen bond interactions.

Crystal structure of methylprednisolone acetate form II, C 24H 32O 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wheatley, Austin M.; Kaduk, James A.; Gindhart, Amy M.

The crystal structure of methylprednisolone acetate form II, C 24H 32O 6, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Methylprednisolone acetate crystallizes in space groupP2 12 12 1(#19) witha= 8.17608(2),b= 9.67944(3),c= 26.35176(6) Å,V= 2085.474(6) Å 3, andZ= 4. Both hydroxyl groups act as hydrogen bond donors, resulting in a two-dimensional hydrogen bond network in theabplane. C–H…O hydrogen bonds also contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1412.

Density functional study of the adsorption of aspirin on the hydroxylated (0 0 1) α-quartz surface

NASA Astrophysics Data System (ADS)

Abbasi, A.; Nadimi, E.; Plänitz, P.; Radehaus, C.

2009-08-01

In this study the adsorption geometry of aspirin molecule on a hydroxylated (0 0 1) α-quartz surface has been investigated using DFT calculations. The optimized adsorption geometry indicates that both, adsorbed molecule and substrate are strongly deformed. Strong hydrogen bonding between aspirin and surface hydroxyls, leads to the breaking of the original hydroxyl-hydroxyl hydrogen bonds (Hydrogenbridges) on the surface. In this case new hydrogen bonds on the hydroxylated (0 0 1) α-quartz surface appear which significantly differ from those at the clean surface. The 1.11 eV adsorption energy reveals that the interaction of aspirin with α-quartz is an exothermic chemical interaction.

Coupled jump rotational dynamics in aqueous nitrate solutions.

PubMed

Banerjee, Puja; Yashonath, Subramanian; Bagchi, Biman

2016-12-21

A nitrate ion (NO 3 - ) with its trigonal planar geometry and charges distributed among nitrogen and oxygen atoms can couple to the extensive hydrogen bond network of water to give rise to unique dynamical characteristics. We carry out detailed atomistic simulations and theoretical analyses to investigate these aspects and report certain interesting findings. We find that the nitrate ions in aqueous potassium nitrate solution exhibit large amplitude rotational jump motions that are coupled to the hydrogen bond rearrangement dynamics of the surrounding water molecules. The jump motion of nitrate ions bears certain similarities to the Laage-Hynes mechanism of rotational jump motions of tagged water molecules in neat liquid water. We perform a detailed atomic-level investigation of hydrogen bond rearrangement dynamics of water in aqueous KNO 3 solution to unearth two distinct mechanisms of hydrogen bond exchange that are instrumental to promote these jump motions of nitrate ions. As observed in an earlier study by Xie et al., in the first mechanism, after breaking a hydrogen bond with nitrate ion, water forms a new hydrogen bond with a water molecule, whereas the second mechanism involves just a switching of hydrogen bond between the two oxygen atoms of the same nitrate ion (W. J. Xie et al., J. Chem. Phys. 143, 224504 (2015)). The magnitude as well as nature of the reorientational jump of nitrate ion for the two mechanisms is different. In the first mechanism, nitrate ion predominantly undergoes out-of-plane rotation, while in the second mechanism, in-plane reorientation of NO 3 - is favourable. These have been deduced by computing the torque on the nitrate ion during the hydrogen bond switching event. We have defined and computed the time correlation function for coupled reorientational jump of nitrate and water and obtained the associated relaxation time which is also different for the two mechanisms. These results provide insight into the relation between the coupled reorientational jump dynamics of solute and solvent molecules.

Influence of hydrogen bond accepting ability of anions on the adsorption performance of ionic liquid surface molecularly imprinted polymers.

PubMed

Zhu, Guifen; Gao, Xia; Wang, Xiaolong; Wang, Jianji; Fan, Jing

2018-01-12

To illuminate the influence mechanism of anionic structure of ionic liquids (ILs) on the adsorption performance of surface molecularly imprinted polymers (MIPs), in this work, six newly designed MIPs were prepared on the surface of amino-poly(styrene-divinylbenzene) particles by using imidazolium ILs with the same cation [C 4 mim] + but different anions (Cl, CH 3 SO 3 , PF 6 , BF 4 , C 4 F 7 O 2 , C 4 F 9 SO 3 ) as template molecules, methacrylic acid as functional monomer, and ethylene dimethacrylate as cross-linker. The resulting MIP materials were characterized by IR and SEM, and the influence of hydrogen bond accepting ability of anions on the adsorption performance of the MIPs for the ILs was investigated in acetonitrile. It was found that adsorption capacity of the MIPs towards the ILs decreased in the order MIP [C4mim][Cl]  > MIP [C4mim][C4F7O2]  ≥ MIP [C4mim][BF4] and MIP [C4mim][CH3SO3]  > MIP [C4mim][C4F9SO3]  > MIP [C4mim][PF6] , which is in good agreement with the ability of anions of the ILs to form hydrogen bonds. Ultraviolet, 1 H-NMR and 35 Cl-NMR spectroscopy was then used to study the interactions of anions of the ILs with the functional monomer. It was found that the hydrogen bond interaction between anions of the ILs and acidic proton of the functional monomer was the main driving force for the high adsorption selectivity of the imprinted polymers, and the stronger hydrogen bond interaction indicates higher binding capacity and higher selectivity of the polymers towards the ILs. It was also verified that the ILs with stronger hydrogen bond accepting ability of anions could be selectively extracted by the corresponding IL-MIPs. These results may provide new insight into the recognition mechanism of MIPs for ILs, and are also useful for the rational design of this new class of imprinting materials. Copyright © 2017 Elsevier B.V. All rights reserved.

Dangling bond defects in SiC: An ab initio study

NASA Astrophysics Data System (ADS)

Tuttle, Blair R.

2018-01-01

We report first-principles microscopic calculations of the properties of defects with dangling bonds in crystalline 3 C -SiC. Specifically, we focus on hydrogenated Si and C vacancies, divacancies, and multivacancies. The latter is a generic model for an isolated dangling bond within a bulk SiC matrix. Hydrogen serves to passivate electrically active defects to allow the isolation of a single dangling-bond defect. We used hybrid density-functional methods to determine energetics and electrical activity. The present results are compared to previous 3 C -SiC calculations and experiments. Finally, we identify homopolar carbon dangling-bond defects as the leakage causing defects in nanoporous SiC alloys.

Enzymatic Functionalization of Carbon-Hydrogen Bonds1

PubMed Central

Lewis, Jared C.; Coelho, Pedro S.

2010-01-01

The development of new catalytic methods to functionalize carbon-hydrogen (C-H) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. In nature, enzymes catalyze regio- and stereoselective C-H bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. The efficiency of these enzymes relative to analogous chemical processes has led to their increased use as biocatalysts in preparative and industrial applications. Furthermore, unlike small molecule catalysts, enzymes can be systematically optimized via directed evolution for a particular application and can be expressed in vivo to augment the biosynthetic capability of living organisms. While a variety of technical challenges must still be overcome for practical application of many enzymes for C-H bond functionalization, continued research on natural enzymes and on novel artificial metalloenzymes will lead to improved synthetic processes for efficient synthesis of complex molecules. In this critical review, we discuss the most prevalent mechanistic strategies used by enzymes to functionalize non-acidic C-H bonds, the application and evolution of these enzymes for chemical synthesis, and a number of potential biosynthetic capabilities uniquely enabled by these powerful catalysts. PMID:21079862

Palladium-Catalyzed Transannular C–H Functionalization of Alicyclic Amines

PubMed Central

Saper, Noam I.; Sanford, Melanie S.

2016-01-01

The discovery of pharmaceutical candidates is a resource-intensive enterprise that frequently requires the parallel synthesis of hundreds or even thousands of molecules. Carbon-hydrogen bonds are present in almost all pharmaceutical agents. As such, the development of selective, rapid, and efficient methods for converting carbon-hydrogen bonds into new chemical entities has the potential to dramatically streamline pharmaceutical development1,2,3,4. Saturated nitrogen-containing heterocycles (alicyclic amines) feature prominently in pharmaceuticals, including treatments for depression (paroxetine, amitifadine), diabetes (gliclazide), leukemia (alvocidib), schizophrenia (risperidone, belaperidone), and nicotine addiction (cytisine and varenicline)5. However, existing methods for the C–H functionalization of saturated nitrogen heterocycles, particularly at sites remote to nitrogen, remain extremely limited 6,7. Here we report a new approach to selectively manipulate the carbon–hydrogen bonds of alicyclic amines at sites remote to nitrogen. Our reaction leverages the boat conformation of the substrates to achieve the palladium-catalyzed amine-directed conversion of C–H bonds to C–C bonds on various alicyclic amine scaffolds. This approach is applied to the synthesis of novel derivatives of several bioactive molecules, including the top-selling smoking cessation drug varenicline (Chantix®). We anticipate that this method should prove broadly useful in medicinal chemistry. PMID:26886789

Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation

PubMed Central

Zheng, Zhong-liang; Ye, Mao-qing; Zuo, Zhen-yu; Liu, Zhi-gang; Tai, Keng-chang; Zou, Guo-lin

2006-01-01

Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33→Ala33, Asp60→Ala60, Ser62→Ala62, and Thr220→Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (ΔΔGT). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the Km values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations. PMID:16411898

Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

PubMed

Zheng, Zhong-liang; Ye, Mao-qing; Zuo, Zhen-yu; Liu, Zhi-gang; Tai, Keng-chang; Zou, Guo-lin

2006-05-01

Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33-->Ala33, Asp60-->Ala60, Ser62-->Ala62, and Thr220-->Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (DeltaDeltaG(T)). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the K(m) values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations.

Hydrogen bonding. Part 25. The nature of the hydrogen bond in hydroxytropenylium chloride (tropone hydrochloride)

NASA Astrophysics Data System (ADS)

Harmon, Kenneth M.; Cross, Joan E.; Toccalino, Patricia L.

1988-08-01

Hydroxytropenylium iodide and bromide contain normal electrostatic OH⋯X - hydrogen bonds. Hydroxytropenylium chloride, however, contains a hydrogen bond intermediate between the normal electrostatic type and the very strong covalent type, similar to the hydrogen bonds found in choline fluoride or the Type I C∞v hydrogen dihalide ions. Infrared comparisons with compounds previously studied demonstrate that the hydroxytropenylium ion is a stronger hydrogen bond donor than either choline cation or protonated betaine cation, and suggest that hydroxytropenylium fluoride, if it can be prepared, should contain a three-center covalent hydrogen bond.

Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions

NASA Astrophysics Data System (ADS)

Miceli, Giacomo; de Gironcoli, Stefano; Pasquarello, Alfredo

2015-01-01

We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers the advantage of simulating liquid water at essentially the same computational cost of standard semilocal functionals. Applied to the water dimer and to ice Ih, we find that the hydrogen-bond energy is only slightly enhanced compared to a standard semilocal functional. We simulate liquid water through molecular dynamics in the NpH statistical ensemble allowing for fluctuations of the system density. The structure of the liquid departs from that found with a semilocal functional leading to more compact structural arrangements. This indicates that the directionality of the hydrogen-bond interaction has a diminished role as compared to the overall attractions, as expected when dispersion interactions are accounted for. This is substantiated through a detailed analysis comprising the study of the partial radial distribution functions, various local order indices, the hydrogen-bond network, and the selfdiffusion coefficient. The explicit treatment of the van der Waals interactions leads to an overall improved description of liquid water.

Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers.

PubMed

Elola, M Dolores; Rodriguez, Javier

2018-06-07

We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.

Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation

PubMed Central

Fitzpatrick, Anthony W.; Knowles, Tuomas P. J.; Waudby, Christopher A.; Vendruscolo, Michele; Dobson, Christopher M.

2011-01-01

Identifying the forces that drive proteins to misfold and aggregate, rather than to fold into their functional states, is fundamental to our understanding of living systems and to our ability to combat protein deposition disorders such as Alzheimer's disease and the spongiform encephalopathies. We report here the finding that the balance between hydrophobic and hydrogen bonding interactions is different for proteins in the processes of folding to their native states and misfolding to the alternative amyloid structures. We find that the minima of the protein free energy landscape for folding and misfolding tend to be respectively dominated by hydrophobic and by hydrogen bonding interactions. These results characterise the nature of the interactions that determine the competition between folding and misfolding of proteins by revealing that the stability of native proteins is primarily determined by hydrophobic interactions between side-chains, while the stability of amyloid fibrils depends more on backbone intermolecular hydrogen bonding interactions. PMID:22022239

Thermal decay of rhodopsin: role of hydrogen bonds in thermal isomerization of 11-cis retinal in the binding site and hydrolysis of protonated Schiff base.

PubMed

Liu, Jian; Liu, Monica Yun; Nguyen, Jennifer B; Bhagat, Aditi; Mooney, Victoria; Yan, Elsa C Y

2009-07-01

Although thermal stability of the G protein-coupled receptor rhodopsin is directly related to its extremely low dark noise level and has recently generated considerable interest, the chemistry behind the thermal decay process of rhodopsin has remained unclear. Using UV-vis spectroscopy and HPLC analysis, we have demonstrated that the thermal decay of rhodopsin involves both hydrolysis of the protonated Schiff base and thermal isomerization of 11-cis to all-trans retinal. Examining the unfolding of rhodopsin by circular dichroism spectroscopy and measuring the rate of thermal isomerization of 11-cis retinal in solution, we conclude that the observed thermal isomerization of 11-cis to all-trans retinal happens when 11-cis retinal is in the binding pocket of rhodopsin. Furthermore, we demonstrate that solvent deuterium isotope effects are involved in the thermal decay process by decreasing the rates of thermal isomerization and hydrolysis, suggesting that the rate-determining step of these processes involves breaking hydrogen bonds. These results provide insight into understanding the critical role of an extensive hydrogen-bonding network on stabilizing the inactive state of rhodopsin and contribute to our current understanding of the low dark noise level of rhodopsin, which enables this specialized protein to function as an extremely sensitive biological light detector. Because similar hydrogen-bonding networks have also been suggested by structural analysis of two other GPCRs, beta1 and beta2 adrenergic receptors, our results could reveal a general role of hydrogen bonds in facilitating GPCR function.

Building a stable RNA U-turn with a protonated cytidine

PubMed Central

Gottstein-Schmidtke, Sina R.; Duchardt-Ferner, Elke; Groher, Florian; Weigand, Julia E.; Gottstein, Daniel; Suess, Beatrix; Wöhnert, Jens

2014-01-01

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5′-UNR-3′ (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3′ phosphate group of the R residue as well as a hydrogen bond between the 2′-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3′ from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone. PMID:24951555

Enhanced hydrogenation activity and diastereomeric interactions of methyl pyruvate co-adsorbed with R-1-(1-naphthyl)ethylamine on Pd(111)

DOE PAGES

Mahapatra, Mausumi; Burkholder, Luke; Garvey, Michael; ...

2016-08-04

Unmodified racemic sites on heterogeneous chiral catalysts reduce their overall enantioselectivity, but this effect is mitigated in the Orito reaction (methyl pyruvate (MP) hydrogenation to methyl lactate) by an increased hydrogenation reactivity. Here, this effect is explored on a R-1-(1-naphthyl)ethylamine (NEA)-modified Pd(111) model catalyst where temperature-programmed desorption experiments reveal that NEA accelerates the rates of both MP hydrogenation and H/D exchange. NEAþMP docking complexes are imaged using scanning tunneling microscopy supplemented by density functional theory calculations to allow the most stable docking complexes to be identified. The results show that diastereomeric interactions between NEA and MP occur predominantly by bindingmore » of the C=C of the enol tautomer of MP to the surface, while simultaneously optimizing C=O...H 2N hydrogen-bonding interactions. In conclusion, the combination of chiral-NEA driven diastereomeric docking with a tautomeric preference enhances the hydrogenation activity since C=C bonds hydrogenate more easily than C=O bonds thus providing a rationale for the catalytic observations.« less

Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin.

PubMed

Liao, Fei; Yuan, Hong; Du, Ke-Jie; You, Yong; Gao, Shu-Qin; Wen, Ge-Bo; Lin, Ying-Wu; Tan, Xiangshi

2016-10-20

A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.

Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

NASA Astrophysics Data System (ADS)

Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

2017-04-01

DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

Matrix isolation studies of hydrogen bonding - An historical perspective

NASA Astrophysics Data System (ADS)

Barnes, Austin J.

2018-07-01

An historical introduction sets matrix isolation in perspective with other spectroscopic techniques for studying hydrogen-bonded complexes. This is followed by detailed accounts of various aspects of hydrogen-bonded complexes that have been studied using matrix isolation spectroscopy: Matrix effects: stabilisation of complexes. Strongly hydrogen-bonded molecular complexes: the vibrational correlation diagram. Anomalous spectra: the Ratajczak-Yaremko model. Metastable complexes. Csbnd H hydrogen bonding and blue shifting hydrogen bonds.

A comparative study between para-aminophenyl and ortho-aminophenyl benzothiazoles using NMR and DFT calculations.

PubMed

Pierens, G K; Venkatachalam, T K; Reutens, D

2014-08-01

Ortho-substituted and para-substituted aminophenyl benzothiazoles were synthesised and characterised using NMR spectroscopy. A comparison of the proton chemical shift values reveals significant differences in the observed chemical shift values for the NH protons indicating the presence of a hydrogen bond in all ortho-substituted compounds as compared to the para compounds. The presence of intramolecular hydrogen bond in the ortho amino substituted aminophenyl benzothiazole forces the molecule to be planar which may be an additional advantage in developing these compounds as Alzheimer's imaging agent because the binding to amyloid fibrils prefers planar compounds. The splitting pattern of the methylene proton next to the amino group also showed significant coupling to the amino proton consistent with the notion of the existence of slow exchange and hydrogen bond in the ortho-substituted compounds. This is further verified by density functional theory calculations which yielded a near planar low energy conformer for all the o-aminophenyl benzothiazoles and displayed a hydrogen bond from the amine proton to the nitrogen of the thiazole ring. A detailed analysis of the (1)H, (13)C and (15)N NMR chemical shifts and density functional theory calculated structures of the compounds are described. Copyright © 2014 John Wiley & Sons, Ltd.

Control of C-H Bond Activation by Mo-Oxo Complexes: pKa or Bond Dissociation Free Energy (BDFE)?

PubMed

Nazemi, Azadeh; Cundari, Thomas R

2017-10-16

A density functional theory (DFT) study (BMK/6-31+G(d)) was initiated to investigate the activation of benzylic carbon-hydrogen bonds by a molybdenum-oxo complex with a potentially redox noninnocent supporting ligand-a simple mimic of the active species of the enzyme ethylbenzene dehydrogenase (EBDH)-through deprotonation (C-H bond heterolysis) or hydrogen atom abstraction (C-H bond homolysis) routes. Activation free-energy barriers for neutral and anionic Mo-oxo complexes were high, but lower for anionic complexes than neutral complexes. Interesting trends as a function of substituents were observed that indicated significant H δ+ character in the transition states (TS), which was further supported by the preference for [2 + 2] addition over HAA for most complexes. Hence, it was hypothesized that C-H activation by these EBDH mimics is controlled more by the pK a than by the bond dissociation free energy of the C-H bond being activated. Therefore, the results suggest promising pathways for designing more efficient and selective catalysts for hydrocarbon oxidation based on EBDH active-site mimics.

6-[6-(Pyridin-2-yl)-1,2,4,5-tetra-zin-3-yl]pyridin-3-amine monohydrate.

PubMed

Broichhagen, Johannes; Klingl, Yvonne E; Trauner, Dirk; Mayer, Peter

2016-02-01

The packing of the title compound, C12H9N7·H2O, is dominated by hydrogen bonding and π-stacking. Layers parallel to [010] are established by hydrogen bonds involving all amine donor functions and one of the water donor functions, while the remaining water donor function enables the stacking of the layers along [10-1], which is accompanied by π-stacking. In the molecule, the plane of the central tetra-zine ring forms angles of 5.33 (7) and 19.84 (8)° with the adjacent 3-amine-pyridine and pyridine rings, respectively.

A theoretical study on the characteristics of the intermolecular interactions in the active site of human androsterone sulphotransferase: DFT calculations of NQR and NMR parameters and QTAIM analysis.

PubMed

Astani, Elahe K; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L

2016-07-01

A theoretical study at the level of density functional theory (DFT) was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond interactions, in the active site of enzyme human androsterone sulphotransferase (SULT2A1/ADT). Geometry optimization, interaction energy, (2)H, (14)N, and (17)O electric field gradient (EFG) tensors, (1)H, (13)C, (17)O, and (15)N chemical shielding (CS) tensors, Natural Bonding Orbital (NBO) analysis, and quantum theory of atoms in molecules (QTAIM) analysis of this active site were investigated. It was found that androsterone (ADT) is able to form hydrogen bonds with residues Ser80, Ile82, and His99 of the active site. The interaction energy calculations and NBO analysis revealed that the ADT molecule forms the strongest hydrogen bond with Ser80. Results revealed that ADT interacts with the other residues through electrostatic and Van der Waals interactions. Results showed that these hydrogen bonds influence on the calculated (2)H, (14)N, and (17)O quadrupole coupling constants (QCCs), as well as (1)H, (13)C, (17)O, and (15)N CS tensors. The magnitude of the QCC and CS changes at each nucleus depends directly on its amount of contribution to the hydrogen bond interaction. Copyright © 2016 Elsevier Inc. All rights reserved.

Spectroscopic investigation on cocrystal formation between adenine and fumaric acid based on infrared and Raman techniques.

PubMed

Du, Yong; Fang, Hong Xia; Zhang, Qi; Zhang, Hui Li; Hong, Zhi

2016-01-15

As an important component of double-stranded DNA, adenine has powerful hydrogen-bond capability, due to rich hydrogen bond donors and acceptors existing within its molecular structure. Therefore, it is easy to form cocrystal between adenine and other small molecules with intermolecular hydrogen-bond effect. In this work, cocrystal of adenine and fumaric acid has been characterized as model system by FT-IR and FT-Raman spectral techniques. The experimental results show that the cocrystal formed between adenine and fumaric acid possesses unique spectroscopical characteristic compared with that of starting materials. Density functional theory (DFT) calculation has been performed to optimize the molecular structures and simulate vibrational modes of adenine, fumaric acid and the corresponding cocrystal. Combining the theoretical and experimental vibrational results, the characteristic bands corresponding to bending and stretching vibrations of amino and carbonyl groups within cocrystal are shifted into lower frequencies upon cocrystal formation, and the corresponding bond lengths show some increase due to the effect of intermolecular hydrogen bonding. Different vibrational modes shown in the experimental spectra have been assigned based on the simulation DFT results. The study could provide experimental and theoretical benchmarks to characterize cocrystal formed between active ingredients and cocrystal formers and also the intermolecular hydrogen-bond effect within cocrystal formation process by vibrational spectroscopic techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide

PubMed Central

Jolley, Elizabeth A.

2017-01-01

Abstract Non-standard nucleotides are ubiquitous in RNA. Thermodynamic studies with RNA duplexes containing non-standard nucleotides, whether incorporated naturally or chemically, can provide insight into the stability of Watson–Crick pairs and the role of specific functional groups in stabilizing a Watson–Crick pair. For example, an A-U, inosine•U and pseudouridine•A pair each form two hydrogen bonds. However, an RNA duplex containing a central I•U pair or central Ψ•A pair is 2.4 kcal/mol less stable or 1.7 kcal/mol more stable, respectively, than the corresponding duplex containing an A-U pair. In the non-standard nucleotide purine, hydrogen replaces the exocyclic amino group of A. This replacement results in a P•U pair containing only one hydrogen bond. Optical melting studies were performed with RNA duplexes containing P•U pairs adjacent to different nearest neighbors. The resulting thermodynamic parameters were compared to RNA duplexes containing A-U pairs in order to determine the contribution of the hydrogen bond involving the exocyclic amino group. Results indicate a loss of 1.78 kcal/mol, on average, when an internal P•U replaces A-U in an RNA duplex. This value is compared to the thermodynamics of a hydrogen bond determined by similar methods. Nearest neighbor parameters were derived for use in free energy and secondary structure prediction software. PMID:28180321

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Choi, Gilbert J.; Zhu, Qilei; Miller, David C.; Gu, Carol J.; Knowles, Robert R.

2016-11-01

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process—a subset of the classical Hofmann-Löffler-Freytag reaction—amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer.

PubMed

Choi, Gilbert J; Zhu, Qilei; Miller, David C; Gu, Carol J; Knowles, Robert R

2016-11-10

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Exploring the Counteracting Mechanism of Trehalose on Urea Conferred Protein Denaturation: A Molecular Dynamics Simulation Study.

PubMed

Paul, Subrata; Paul, Sandip

2015-07-30

To provide the underlying mechanism of the inhibiting effect of trehalose on the urea denatured protein, we perform classical molecular dynamics simulations of N-methylacetamide (NMA) in aqueous urea and/or trehalose solution. The site-site radial distribution functions and hydrogen bond properties indicate in binary urea solution the replacement of NMA-water hydrogen bonds by NMA-urea hydrogen bonds. On the other hand, in ternary urea and trehalose solution, trehalose does not replace the NMA-urea hydrogen bonds significantly; rather, it forms hydrogen bonds with the NMA molecule. The calculation of a preferential interaction parameter shows that, at the NMA surface, trehalose molecules are preferred and the preference for urea decreases slightly in ternary solution with respect to the binary solution. The exclusion of urea molecules in the ternary urea-NMA-trehalose system causes alleviation in van der Waals interaction energy between urea and NMA molecules. Our findings also reveal the following: (a) trehalose and urea induced second shell collapse of water structure, (b) a reduction in the mean trehalose cluster size in ternary solution, and (c) slowing down of translational motion of solution species in the presence of osmolytes. Implications of these results for the molecular explanations of the counteracting mechanism of trehalose on urea induced protein denaturation are discussed.

The excited-state intramolecular proton transfer in Nsbnd H-type dye molecules with a seven-membered-ring intramolecular hydrogen bond: A theoretical insight

NASA Astrophysics Data System (ADS)

Yuan, Huijuan; Feng, Songyan; Wen, Keke; Guo, Xugeng; Zhang, Jinglai

2018-02-01

Excited-state intramolecular proton transfer (ESIPT) reactions of a series of N(R)sbnd H ⋯ N-type seven-membered-ring hydrogen-bonding compounds were explored by employing density functional theory/time-dependent density functional theory calculations with the PBE0 functional. Our results indicate that the absorption and emission spectra predicted theoretically match very well the experimental findings. Additionally, as the electron-withdrawing strength of R increases, the intramolecular H-bond of the Nsbnd S1 form gradually enhances, and the forward energy barrier along the ESIPT reaction gradually decreases. For compound 4, its ESIPT reaction is found to be a barrierless process due to the involvement of a strong electron-withdrawing COCF3 group. It is therefore a reasonable presumption that the ESIPT efficiency of these N(R)sbnd H ⋯ N-type seven-membered-ring H-bonding systems can be improved when a strong electron-withdrawing group in R is introduced.

Ab initio characterization of coupling strength for all types of dangling-bond pairs on the hydrogen-terminated Si(100)-2 × 1 surface

NASA Astrophysics Data System (ADS)

Shaterzadeh-Yazdi, Zahra; Sanders, Barry C.; DiLabio, Gino A.

2018-04-01

Recent work has suggested that coupled silicon dangling bonds sharing an excess electron may serve as building blocks for quantum-cellular-automata cells and quantum computing schemes when constructed on hydrogen-terminated silicon surfaces. In this work, we employ ab initio density-functional theory to examine the details associated with the coupling between two dangling bonds sharing one excess electron and arranged in various configurations on models of phosphorous-doped hydrogen-terminated silicon (100) surfaces. Our results show that the coupling strength depends strongly on the relative orientation of the dangling bonds on the surface and on the separation between them. The orientation of dangling bonds is determined by the anisotropy of the silicon (100) surface, so this feature of the surface is a significant contributing factor to variations in the strength of coupling between dangling bonds. The results demonstrate that simple models for approximating tunneling, such as the Wentzel-Kramer-Brillouin method, which do not incorporate the details of surface structure, are incapable of providing reasonable estimates of tunneling rates between dangling bonds. The results provide guidance to efforts related to the development of dangling-bond based computing elements.

Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.

PubMed

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2017-06-07

We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH 2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

Selective sp3 C-H alkylation via polarity-match-based cross-coupling.

PubMed

Le, Chip; Liang, Yufan; Evans, Ryan W; Li, Ximing; MacMillan, David W C

2017-07-06

The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp 3 )-C(sp 2 ) coupling, there is a growing demand for C-H alkylation reactions, wherein sp 3 C-H bonds are replaced with sp 3 C-alkyl groups. Here we describe a polarity-match-based selective sp 3 C-H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C-H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl-alkyl fragment coupling. The sp 3 C-H alkylation is highly selective for the α-C-H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry.

Selective sp3 C–H alkylation via polarity-match-based cross-coupling

PubMed Central

Le, Chip; Liang, Yufan; Evans, Ryan W.; Li, Ximing; MacMillan, David W. C.

2017-01-01

The functionalization of carbon–hydrogen (C–H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence1. Although many C–H functionalization reactions involve C(sp3)–C(sp2) coupling, there is a growing demand for C–H alkylation reactions, wherein sp3 C–H bonds are replaced with sp3 C–alkyl groups. Here we describe a polarity-match-based selective sp3 C–H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C–H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl–alkyl fragment coupling. The sp3 C–H alkylation is highly selective for the α-C–H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry. PMID:28636596

Theoretical vibrational sum-frequency generation spectroscopy of water near lipid and surfactant monolayer interfaces. II. Two-dimensional spectra.

PubMed

Roy, S; Gruenbaum, S M; Skinner, J L

2014-12-14

The structural stability and function of biomolecules is strongly influenced by the dynamics and hydrogen bonding of interfacial water. Understanding and characterizing the dynamics of these water molecules require a surface-sensitive technique such as two-dimensional vibrational sum-frequency generation (2DSFG) spectroscopy. We have combined theoretical 2DSFG calculations with molecular dynamics simulations in order to investigate the dynamics of water near different lipid and surfactant monolayer surfaces. We show that 2DSFG can distinguish the dynamics of interfacial water as a function of the lipid charge and headgroup chemistry. The dynamics of water is slow compared to the bulk near water-zwitterionic and water-anionic interfaces due to conformational constraints on interfacial water imposed by strong phosphate-water hydrogen bonding. The dynamics of water is somewhat faster near water-cationic lipid interfaces as no such constraint is present. Using hydrogen bonding and rotational correlation functions, we characterize the dynamics of water as a function of the distance from the interface between water and zwitterionic lipids. We find that there is a transition from bulk-like to interface-like dynamics approximately 7 Å away from a zwitterionic phosphatidylcholine monolayer surface.

Selective sp3 C-H alkylation via polarity-match-based cross-coupling

NASA Astrophysics Data System (ADS)

Le, Chip; Liang, Yufan; Evans, Ryan W.; Li, Ximing; MacMillan, David W. C.

2017-07-01

The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp3)-C(sp2) coupling, there is a growing demand for C-H alkylation reactions, wherein sp3 C-H bonds are replaced with sp3 C-alkyl groups. Here we describe a polarity-match-based selective sp3 C-H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C-H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl-alkyl fragment coupling. The sp3 C-H alkylation is highly selective for the α-C-H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry.

Structure and energetics of hydrogen-bonded networks of methanol on close packed transition metal surfaces

NASA Astrophysics Data System (ADS)

Murphy, Colin J.; Carrasco, Javier; Lawton, Timothy J.; Liriano, Melissa L.; Baber, Ashleigh E.; Lewis, Emily A.; Michaelides, Angelos; Sykes, E. Charles H.

2014-07-01

Methanol is a versatile chemical feedstock, fuel source, and energy storage material. Many reactions involving methanol are catalyzed by transition metal surfaces, on which hydrogen-bonded methanol overlayers form. As with water, the structure of these overlayers is expected to depend on a delicate balance of hydrogen bonding and adsorbate-substrate bonding. In contrast to water, however, relatively little is known about the structures methanol overlayers form and how these vary from one substrate to another. To address this issue, herein we analyze the hydrogen bonded networks that methanol forms as a function of coverage on three catalytically important surfaces, Au(111), Cu(111), and Pt(111), using a combination of scanning tunneling microscopy and density functional theory. We investigate the effect of intermolecular interactions, surface coverage, and adsorption energies on molecular assembly and compare the results to more widely studied water networks on the same surfaces. Two main factors are shown to direct the structure of methanol on the surfaces studied: the surface coverage and the competition between the methanol-methanol and methanol-surface interactions. Additionally, we report a new chiral form of buckled hexamer formed by surface bound methanol that maximizes the interactions between methanol monomers by sacrificing interactions with the surface. These results serve as a direct comparison of interaction strength, assembly, and chirality of methanol networks on Au(111), Cu(111), and Pt(111) which are catalytically relevant for methanol oxidation, steam reforming, and direct methanol fuel cells.

Theoretical study of interactions between cysteine and perfluoropropanoic acid in gas and aqueous phase

NASA Astrophysics Data System (ADS)

Holmes, Tiffani M.; Doskocz, Jacek; Wright, Terrance; Hill, Glake A.

The interaction of perfluoropropanoic acid (PFPA) with the amino acid cysteine was investigated using density functional theory. Previous studies suggest that the peroxisome proliferator chemical, perfluorooctanoic acid, is circulated throughout the body by way of sulfur-containing amino acids. We present conformational analysis of the interactions of PFPA, a small model of perfluorooctanoic acid, with the sulfur-containing amino acid which occur by the process of hydrogen bonding, in which the hydrogen of the sulfhydryl group interacts with the carboxyl oxygen, and the amino nitrogen forms a hydrogen bond with the hydrogen of the bond OH group of the fluorinated alkyl. We also show in our structures a recently characterized weak nonbonded interaction between divalent sulfur and a main chain carboxyl oxygen in proteins. B3LYP calculated free energies and interaction energies predict low-energy, high-interaction conformations for complex systems of perfluorinated fatty acid interactions with cysteine.

Density functional theory analysis of the impact of steric interaction on the function of switchable polarity solvents

DOE PAGES

McNally, Joshua S.; Noll, Bruce; Orme, Christopher J.; ...

2015-05-04

Here, a density functional theory (DFT) analysis has been performed to explore the impact of steric interactions on the function of switchable polarity solvents (SPS) and their implications on a quantitative structure-activity relationship (QSAR) model previously proposed for SPS. An x-ray crystal structure of the N,N-dimethylcyclohexylammonium bicarbonate (Hdmcha) salt has been solved as an asymmetric unit containing two cation/anion pairs, with a hydrogen bonding interaction observed between the bicarbonate anions, as well as between the cation and anion in each pair. DFT calculations provide an optimized structure of Hdmcha that closely resembles experimental data and reproduces the cation/anion interaction withmore » the inclusion of a dielectric field. Relaxed potential energy surface (PES) scans have been performed on Hdmcha-based computational model compounds, differing in the size of functional group bonded to the nitrogen center, to assess the steric impact of the group on the relative energy and structural properties of the compound. Results suggest that both the length and amount of branching associated with the substituent impact the energetic limitations on rotation of the group along the N-R bond and NC-R bond, and disrupt the energy minimized position of the hydrogen bonded bicarbonate group. The largest interaction resulted from functional groups that featured five bonds between the ammonium proton and a proton on a functional group with the freedom of rotation to form a pseudo-six membered ring which included both protons.« less

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers.

PubMed

Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

2010-12-09

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers

PubMed Central

Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

2010-01-01

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs. PMID:21197382

Hydrogen and dihydrogen bonding of transition metal hydrides

NASA Astrophysics Data System (ADS)

Jacobsen, Heiko

2008-04-01

Intermolecular interactions between a prototypical transition metal hydride WH(CO) 2NO(PH 3) 2 and a small proton donor H 2O have been studied using DFT methodology. The hydride, nitrosyl and carbonyl ligand have been considered as site of protonation. Further, DFT-D calculations in which empirical corrections for the dispersion energy are included, have been carried out. A variety of pure and hybrid density functionals (BP86, PW91, PBE, BLYP, OLYP, B3LYP, B1PW91, PBE0, X3LYP) have been considered, and our calculations indicate the PBE functional and its hybrid variation are well suited for the calculation of transition metal hydride hydrogen and dihydrogen bonding. Dispersive interactions make up for a sizeable portion of the intermolecular interaction, and amount to 20-30% of the bond energy and to 30-40% of the bond enthalpy. An energy decomposition analysis reveals that the H⋯H bond of transition metal hydrides contains both covalent and electrostatic contributions.

Conjugated π electron engineering of generalized stacking fault in graphene and h-BN.

PubMed

Ouyang, Bin; Chen, Cheng; Song, J

2018-03-02

Generalized-stacking-fault energy (GSFE) serves as an important metric that prescribes dislocation behaviors in materials. In this paper, utilizing first-principle calculations and chemical bonding analysis, we studied the behaviors of generalized stacking fault in graphene and h-BN. It has been shown that the π bond formation plays a critical role in the existence of metastable stacking fault (MSF) in graphene and h-BN lattice along certain slip directions. Chemical functionalization was then proposed as an effective means to engineer the π bond, and subsequently MSF along dislocation slips within graphene and h-BN. Taking hydrogenation as a representative functionalization method, we demonstrated that, with the preferential adsorption of hydrogen along the slip line, π electrons along the slip would be saturated by adsorbed hydrogen atoms, leading to the moderation or elimination of MSF. Our study elucidates the atomic mechanism of MSF formation in graphene-like materials, and more generally, provides important insights towards predictive tuning of mechanic properties in two-dimensional nanomaterials.

Conjugated π electron engineering of generalized stacking fault in graphene and h-BN

NASA Astrophysics Data System (ADS)

Ouyang, Bin; Chen, Cheng; Song, J.

2018-03-01

Generalized-stacking-fault energy (GSFE) serves as an important metric that prescribes dislocation behaviors in materials. In this paper, utilizing first-principle calculations and chemical bonding analysis, we studied the behaviors of generalized stacking fault in graphene and h-BN. It has been shown that the π bond formation plays a critical role in the existence of metastable stacking fault (MSF) in graphene and h-BN lattice along certain slip directions. Chemical functionalization was then proposed as an effective means to engineer the π bond, and subsequently MSF along dislocation slips within graphene and h-BN. Taking hydrogenation as a representative functionalization method, we demonstrated that, with the preferential adsorption of hydrogen along the slip line, π electrons along the slip would be saturated by adsorbed hydrogen atoms, leading to the moderation or elimination of MSF. Our study elucidates the atomic mechanism of MSF formation in graphene-like materials, and more generally, provides important insights towards predictive tuning of mechanic properties in two-dimensional nanomaterials.

Automatic superposition of drug molecules based on their common receptor site

NASA Astrophysics Data System (ADS)

Kato, Yuichi; Inoue, Atsushi; Yamada, Miho; Tomioka, Nobuo; Itai, Akiko

1992-10-01

We have prevously developed a new rational method for superposing molecules in terms of submolecular physical and chemical properties, but not in terms of atom positions or chemical structures as has been done in the conventional methods. The program was originally developed for interactive use on a three-dimensional graphic display, providing goodness-of-fit indices on molecular shape, hydrogen bonds, electrostatic interactions and others. Here, we report a new unbiased searching method for the best superposition of molecules, covering all the superposing modes and conformational freedom, as an additional function of the program. The function is based on a novel least-squares method which superposes the expected positions and orientations of hydrogen bonding partners in the receptor that are deduced from both molecules. The method not only gives reliability and reproducibility to the result of the superposition, but also allows us to save labor and time. It is demonstrated that this method is very efficient for finding the correct superposing mode in such systems where hydrogen bonds play important roles.

Hydrogen bonding between nitriles and hydrogen halides and the topological properties of molecular charge distributions

NASA Astrophysics Data System (ADS)

Boyd, Russell J.; Choi, Sai Cheng

1986-08-01

The topological properties of the charge density of the hydrogen-bonded complexes between nitrites and hydrogen chloride correlate linearly with theoretical estimates of the hydrogen-bond energy. At the 6-31G ** level, the hydrogenbond energies range from a low of 10 kJ/mol m NCCN—HC1 to a high of 38 kJ/mol in LiCN—HCl. A linear relationship between the charge density at the hydrogen-bond critical point and the NH internuclear distance of the RCN—HC1 complexes indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader, Tang, Tal and Biegler-König can be extended to intermolecular hydrogen bonding.

Free energy of adhesion of lipid bilayers on silica surfaces

NASA Astrophysics Data System (ADS)

Schneemilch, M.; Quirke, N.

2018-05-01

The free energy of adhesion per unit area (hereafter referred to as the adhesion strength) of lipid arrays on surfaces is a key parameter that determines the nature of the interaction between materials and biological systems. Here we report classical molecular simulations of water and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayers at model silica surfaces with a range of silanol densities and structures. We employ a novel technique that enables us to estimate the adhesion strength of supported lipid bilayers in the presence of water. We find that silanols on the silica surface form hydrogen bonds with water molecules and that the water immersion enthalpy for all surfaces varies linearly with the surface density of these hydrogen bonds. The adhesion strength of lipid bilayers is a linear function of the surface density of hydrogen bonds formed between silanols and the lipid molecules on crystalline surfaces. Approximately 20% of isolated silanols form such bonds but more than 99% of mutually interacting geminal silanols do not engage in hydrogen bonding with water. On amorphous silica, the bilayer displays much stronger adhesion than expected from the crystalline surface data. We discuss the implications of these results for nanoparticle toxicity.

Polarization response of clathrate hydrates capsulated with guest molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng, Qun; Li, Jinshan, E-mail: ljs915@263.net, E-mail: myang@scu.edu.cn; Huang, Hui

2016-05-28

Clathrate hydrates are characterized by their water cages encapsulating various guest atoms or molecules. The polarization effect of these guest-cage complexes was studied with combined density functional theory and finite-field calculations. An addition rule was noted for these systems whose total polarizability is approximately equal to the polarizability sum of the guest and the cage. However, their distributional polarizability computed with Hirshfeld partitioning scheme indicates that the guest–cage interaction has considerable influence on their polarization response. The polarization of encapsulated guest is reduced while the polarization of water cage is enhanced. The counteraction of these two opposite effects leads tomore » the almost unchanged total polarizability. Further analysis reveals that the reduced polarizability of encapsulated guest results from the shielding effect of water cage against the external field and the enhanced polarizability of water cage from the enhanced bonding of hydrogen bonds among water molecules. Although the charge transfer through the hydrogen bonds is rather small in the water cage, the polarization response of clathrate hydrates is sensitive to the changes of hydrogen bonding strength. The guest encapsulation strengthens the hydrogen bonding network and leads to enhanced polarizability.« less

The role of boron nitride nanotube as a new chemical sensor and potential reservoir for hydrogen halides environmental pollutants

NASA Astrophysics Data System (ADS)

Yoosefian, Mehdi; Etminan, Nazanin; Moghani, Maryam Zeraati; Mirzaei, Samaneh; Abbasi, Shima

2016-10-01

Density functional theory (DFT) studies on the interaction of hydrogen halides (HX) environmental pollutants and the boron nitride nanotubes (BNNTs) have been reported. To exploit the possibility of BNNTs as gas sensors, the adsorption of hydrogen fluoride (HF), hydrogen chloride (HCl) and hydrogen bromide (HBr) on the side wall of armchair (5,5) boron nitride nanotubes have been investigated. B3LYP/6-31G (d) level were used to analyze the structural and electronic properties of investigate sensor. The adsorption process were interpreted by highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO), quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) and molecular electrostatic potential (MEP) analysis. Topological parameters of bond critical points have been used to calculate as measure of hydrogen bond (HB) strength. Stronger binding energy, larger charge transfer and charge density illustrate that HF gas possesses chemisorbed adsorption process. The obtained results also show the strongest HB in HF/BNNT complex. We expect that results could provide helpful information for the design of new BNNTs based sensing devices.

Density functional theory study of hydrogen atom abstraction from a series of para-substituted phenols: why is the Hammett σ(p)+ constant able to represent radical reaction rates?

PubMed

Yoshida, Tatsusada; Hirozumi, Koji; Harada, Masataka; Hitaoka, Seiji; Chuman, Hiroshi

2011-06-03

The rate of hydrogen atom abstraction from phenolic compounds by a radical is known to be often linear with the Hammett substitution constant σ(+), defined using the S(N)1 solvolysis rates of substituted cumyl chlorides. Nevertheless, a physicochemical reason for the above "empirical fact" has not been fully revealed. The transition states of complexes between the 2,2-diphenyl-1-picrylhydrazyl radical (dpph·) and a series of para-substituted phenols were determined by DFT (Density Functional Theory) calculations, and then the activation energy as well as the homolytic bond dissociation energy of the O-H bond and charge distribution in the transition state were calculated. The heterolytic bond dissociation energy of the C-Cl bond and charge distribution in the corresponding para-substituted cumyl chlorides were calculated in parallel. Excellent correlations among σ(+), charge distribution, and activation and bond dissociation energies revealed quantitatively that there is a strong similarity between the two reactions, showing that the electron-deficiency of the π-electron system conjugated with a substituent plays a crucial role in determining rates of the two reactions. The results provide a new insight into and physicochemical understanding of σ(+) in the hydrogen abstraction from substituted phenols by a radical.

Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra.

PubMed

Lee, Christopher M; Kubicki, James D; Fan, Bingxin; Zhong, Linghao; Jarvis, Michael C; Kim, Seong H

2015-12-10

Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

Building a stable RNA U-turn with a protonated cytidine.

PubMed

Gottstein-Schmidtke, Sina R; Duchardt-Ferner, Elke; Groher, Florian; Weigand, Julia E; Gottstein, Daniel; Suess, Beatrix; Wöhnert, Jens

2014-08-01

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone. © 2014 Gottstein-Schmidtke et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

How Do Organic Chemistry Students Understand and Apply Hydrogen Bonding?

NASA Astrophysics Data System (ADS)

Henderleiter, J.; Smart, R.; Anderson, J.; Elian, O.

2001-08-01

Students completing a year-long organic chemistry sequence were interviewed to assess how they understood, explained, and applied knowledge of hydrogen bonding to the physical behavior of molecules. Students were asked to define hydrogen bonding and explain situations in which hydrogen bonding could occur. They were asked to predict and explain how hydrogen bonding influences boiling point, the solubility of molecules, and NMR and IR spectra. Results suggest that although students may be able to give appropriate definitions of hydrogen bonding and may recognize when this phenomenon can occur, significant numbers cannot apply their knowledge of hydrogen bonding to physical properties of molecules or to the interpretation of spectral data. Some possess misconceptions concerning boiling points and the ability of molecules to induce hydrogen bonding. Instructional strategies must be adjusted to address these issues.

Hydrogen-bonded diketopyrrolopyrrole (DPP) pigments as organic semiconductors

DOE PAGES

Glowacki, Eric Daniel; Coskun, Halime; Blood-Forsythe, Martin A.; ...

2014-10-13

Diketopyrrolopyrroles (DPPs) have recently gained attention as building-blocks for organic semiconducting polymers and small molecules, however the semiconducting properties of their hydrogen-bonded (H-bonded) pigment forms have not been explored. Herein we report on the performance of three archetypical H-bonded DPP pigments, which show ambipolar carrier mobilities in the range 0.01–0.06 cm 2/V s in organic field-effect transistors. Their semiconducting properties are correlated with crystal structure, where an H-bonded crystal lattice supports close and relatively cofacial π–π stacking. To better understand transport in these systems, density functional theory calculations were carried out, indicating theoretical maximum ambipolar mobility values of ~0.3 cmmore » 2/V s. Furthermore, based on these experimental and theoretical results, H-bonded DPPs represent a viable alternative to more established DPP-containing polymers and small molecules where H-bonding is blocked by N-alkylation.« less

Selective Hydrogen Atom Abstraction through Induced Bond Polarization: Direct α-Arylation of Alcohols through Photoredox, HAT, and Nickel Catalysis.

PubMed

Twilton, Jack; Christensen, Melodie; DiRocco, Daniel A; Ruck, Rebecca T; Davies, Ian W; MacMillan, David W C

2018-05-04

The combination of nickel metallaphotoredox catalysis, hydrogen atom transfer catalysis, and a Lewis acid activation mode, has led to the development of an arylation method for the selective functionalization of alcohol α-hydroxy C-H bonds. This approach employs zinc-mediated alcohol deprotonation to activate α-hydroxy C-H bonds while simultaneously suppressing C-O bond formation by inhibiting the formation of nickel alkoxide species. The use of Zn-based Lewis acids also deactivates other hydridic bonds such as α-amino and α-oxy C-H bonds. This approach facilitates rapid access to benzylic alcohols, an important motif in drug discovery. A 3-step synthesis of the drug Prozac exemplifies the utility of this new method. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Facile Synthesis and Superior Catalytic Activity of Nano-TiN@N-C for Hydrogen Storage in NaAlH4.

PubMed

Zhang, Xin; Ren, Zhuanghe; Lu, Yunhao; Yao, Jianhua; Gao, Mingxia; Liu, Yongfeng; Pan, Hongge

2018-05-09

Herein, we synthesize successfully ultrafine TiN nanoparticles (<3 nm in size) embedded in N-doped carbon nanorods (nano-TiN@N-C) by a facile one-step calcination process. The prepared nano-TiN@N-C exhibits superior catalytic activity for hydrogen storage in NaAlH 4 . Adding 7 wt % nano-TiN@N-C induces more than 100 °C reduction in the onset dehydrogenation temperature of NaAlH 4 . Approximately 4.9 wt % H 2 is rapidly released from the 7 wt % nano-TiN@N-C-containing NaAlH 4 at 140 °C within 60 min, and the dehydrogenation product is completely hydrogenated at 100 °C within 15 min under 100 bar of hydrogen, exhibiting significantly improved desorption/absorption kinetics. No capacity loss is observed for the nano-TiN@N-C-containing sample within 25 de-/hydrogenation cycles because nano-TiN functions as an active catalyst instead of a precursor. A severe structural distortion with extended bond lengths and reduced bond strengths for Al-H bonding when the [AlH 4 ] - group adsorbs on the TiN cluster is demonstrated for the first time by density functional theory calculations, which well-explains the reduced de-/hydrogenation temperatures of the nano-TiN@N-C-containing NaAlH 4 . These findings provide new insights into designing and synthesizing high-performance catalysts for hydrogen storage in complex hydrides.

6-[6-(Pyridin-2-yl)-1,2,4,5-tetra­zin-3-yl]pyridin-3-amine monohydrate

PubMed Central

Broichhagen, Johannes; Klingl, Yvonne E.; Trauner, Dirk; Mayer, Peter

2016-01-01

The packing of the title compound, C12H9N7·H2O, is dominated by hydrogen bonding and π-stacking. Layers parallel to [010] are established by hydrogen bonds involving all amine donor functions and one of the water donor functions, while the remaining water donor function enables the stacking of the layers along [10-1], which is accompanied by π-stacking. In the molecule, the plane of the central tetra­zine ring forms angles of 5.33 (7) and 19.84 (8)° with the adjacent 3-amine-pyridine and pyridine rings, respectively. PMID:26958397

One-shot preparation of an inherently chiral trifunctional calix[4]arene from an easily available cone-triformylcalix[4]arene.

PubMed

Ciaccia, Maria; Tosi, Irene; Cacciapaglia, Roberta; Casnati, Alessandro; Baldini, Laura; Di Stefano, Stefano

2013-06-14

Via selective 1,3-distal intramolecular Cannizzaro disproportionation of an easily available cone-triformylcalix[4]arene, an inherently chiral trifunctional cone-calix[4]arene derivative has been prepared. The presence of three different functional groups (-CH2OH, -CHO and -COOH) at the upper rim of the calixarene scaffold makes this compound a versatile intermediate for the development of multifunctional devices. Interesting chiral discrimination of serine derivatives has been observed, presumably thanks to a multipoint-interaction involving the reversible imine bond formation and the hydrogen bonding of the hydroxyl group of the amino acid side-chain with the upper rim functional groups. Consistently, chiral discrimination was not observed with alanine and valine derivatives, lacking hydrogen bonding groups on the side-chain.

A high level Ab initio study of the anionic hydrogen-bonded complexes FH-CN-, FH-NC-, H2O-CN- and H2O-NC-

NASA Technical Reports Server (NTRS)

Lee, Timothy J.

1989-01-01

HF, H2O, CN- and their hydrogen-bonded complexes were studied using state-of-the-art ab initio quantum mechanical methods. A large Gaussian one particle basis set consisting of triple zeta plus double polarization plus diffuse s and p functions (TZ2P + diffuse) was used. The theoretical methods employed include self consistent field, second order Moller-Plesset perturbation theory, singles and doubles configuration interaction theory and the singles and doubles coupled cluster approach. The FH-CN- and FH-NC- and H2O-CN-, H2O-NC- pairs of complexes are found to be essentially isoenergetic. The first pair of complexes are predicted to be bound by approx. 24 kcal/mole and the latter pair bound by approximately 15 kcal/mole. The ab initio binding energies are in good agreement with the experimental values. The two being shorter than the analogous C-N hydrogen bond. The infrared (IR) spectra of the two pairs of complexes are also very similar, though a severe perturbation of the potential energy surface by proton exchange means that the accurate prediction of the band center of the most intense IR mode requires a high level of electronic structure theory as well as a complete treatment of anharmonic effects. The bonding of anionic hydrogen-bonded complexes is discussed and contrasted with that of neutral hydrogen-bonded complexes.

Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

NASA Astrophysics Data System (ADS)

Plastun, Inna L.; Agandeeva, Ksenia E.; Bokarev, Andrey N.; Zenkin, Nikita S.

2017-03-01

Intermolecular interaction of diamond-like nanoparticles and flavonoids is investigated by numerical simulation. Using molecular modelling by the density functional theory method, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and nanodiamonds surrounded with carboxylic groups. Enriched adamantane (1,3,5,7 - adamantanetetracarboxylic acid) is used as an example of diamond-like nanoparticles. Intermolecular forces and structure of hydrogen bonds are investigated. IR - spectra and structure parameters of quercetin - adamantanetetracarboxylic acid molecular complex are obtained by numerical simulation using the Gaussian software complex. Received data coincide well with experimental results. Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex are examined. Possibilities of flavonoids interaction with DNA at the molecular level are also considered.

Hydrogen-bonding interactions between a nitrile-based functional ionic liquid and DMSO

NASA Astrophysics Data System (ADS)

Zheng, Yan-Zhen; Zhou, Yu; Deng, Geng; Yu, Zhi-Wu

2016-11-01

Task-specific ionic liquids (TSILs) have been introduced by incorporating additional functional groups in the cation or anion to impart specific properties or reactivates. In this work, the hydrogen-bonding interactions between a nitrile-functional TSIL 1-propylnitrile-3-methylimidazolium tetrafluoroborate ([PCNMIM][BF4]) and dimethyl sulphoxide (DMSO) were investigated in detail by attenuated total reflection infrared spectroscopy (ATR-IR), combined with hydrogen nuclear magnetic resonance (1H NMR) and density functional theory calculations (DFT). It was found that, first, introducing a nitrile group into the alkyl chain does not change the main interaction site in the cation. It is still the C2 hydrogen. So the v(C2-H) is more sensitive to the environmental change and can be used as an indicator of the environments change of IL. Second, the wavenumber shift changes of v(C2-H) have two turning points (xDMSO ≈ 0.6 and 0.9), dividing the dilution process into three stages. Combined with the calculation results, the dilution process is identified as: From larger ion clusters to smaller ion clusters (xDMSO < 0.6), then to ion pairs (0.6 0.9). Introducing a nitrile group into the alkyl chain does not influence the dilution process of IL dissolving in DMSO. Third, the Ctbnd N in [PCNMIM][BF4] can work as an electron donor in forming hydrogen-bonds with the methyl group of [PCNMIM]+ and DMSO, but its strength is weaker than that formed by the imidazolium ring C-Hs. The dual roles of the cation to work as both electron acceptor and donor expand the wide applications of this nitrile-functional ionic liquid.

Molecular Dynamics Simulation of Mahkota Dewa (Phaleria Macrocarpa) Extract in Subcritical Water Extraction Process

NASA Astrophysics Data System (ADS)

Hashim, N. A.; Mudalip, S. K. Abdul; Harun, N.; Che Man, R.; Sulaiman, S. Z.; Arshad, Z. I. M.; Shaarani, S. M.

2018-05-01

Mahkota Dewa (Phaleria Macrocarpa), a good source of saponin, flavanoid, polyphenol, alkaloid, and mangiferin has an extensive range of medicinal effects. The intermolecular interactions between solute and solvents such as hydrogen bonding considered as an important factor that affect the extraction of bioactive compounds. In this work, molecular dynamics simulation was performed to elucidate the hydrogen bonding exists between Mahkota Dewa extracts and water during subcritical extraction process. A bioactive compound in the Mahkota Dewa extract, namely mangiferin was selected as a model compound. The simulation was performed at 373 K and 4.0 MPa using COMPASS force field and Ewald summation method available in Material Studio 7.0 simulation package. The radial distribution functions (RDF) between mangiferin and water signify the presence of hydrogen bonding in the extraction process. The simulation of the binary mixture of mangiferin:water shows that strong hydrogen bonding was formed. It is suggested that, the intermolecular interaction between OH2O••HMR4(OH1) has been identified to be responsible for the mangiferin extraction process.

Measuring the relative hydrogen-bonding strengths of alcohols in aprotic organic solvents.

PubMed

Tessensohn, Malcolm E; Lee, Melvyn; Hirao, Hajime; Webster, Richard D

2015-01-12

Voltammetric experiments with 9,10-anthraquinone and 1,4-benzoquinone performed under controlled moisture conditions indicate that the hydrogen-bond strengths of alcohols in aprotic organic solvents can be differentiated by the electrochemical parameter ΔEp (red) =|Ep (red(1)) -Ep (red(2)) |, which is the potential separation between the two one-electron reduction processes. This electrochemical parameter is inversely related to the strength of the interactions and can be used to differentiate between primary, secondary, tertiary alcohols, and even diols, as it is sensitive to both their steric and electronic properties. The results are highly reproducible across two solvents with substantially different hydrogen-bonding properties (CH3 CN and CH2 Cl2 ) and are supported by density functional theory calculations. This indicates that the numerous solvent-alcohol interactions are less significant than the quinone-alcohol hydrogen-bonding interactions. The utility of ΔEp (red) was illustrated by comparisons between 1) 3,3,3-trifluoro-n-propanol and 1,3-difluoroisopropanol and 2) ethylene glycol and 2,2,2-trifluoroethanol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Density functional theory study of the reaction mechanism for competitive carbon-hydrogen and carbon-halogen bond activations catalyzed by transition metal complexes.

PubMed

Yang, Xinzheng; Hall, Michael B

2009-03-12

Carbon-hydrogen and carbon-halogen bond activations between halobenzenes and metal centers were studied by density functional theory with the nonempirical meta-GGA Tao-Perdew-Staroverov-Scuseria functional and an all-electron correlation-consistent polarized valence double-zeta basis set. Our calculations demonstrate that the hydrogen on the metal center and halogen in halobenzene could exchange directly through a kite-shaped transition state. Transition states with this structure were previously predicted to have high energy barriers (J. Am. Chem. Soc. 2005, 127, 279), and this prediction misled others in proposing a mechanism for their recent experimental study (J. Am. Chem. Soc. 2006, 128, 3303). Furthermore, other halo-carbon activation pathways were found in the detailed mechanism for the competitive reactions between cationic titanium hydride complex [Cp*((t)Bu(3)P=N)TiH](+) and chlorobenzene under different pressure of H(2). These pathways include the ortho-C-H and Ti-H bond activations for the formation and release of H(2) and the indirect C-Cl bond activation via beta-halogen elimination for the movement of the C(6)H(4) ring and the formation of a C-N bond in the observed final product. A new stable isomer of the observed product with a similar total energy and an unexpected bridging between the Cp* ring and the metal center by a phenyl ring is also predicted.

An energetic scale for equilibrium H/D fractionation factors illuminates hydrogen bond free energies in proteins

PubMed Central

Cao, Zheng; Bowie, James U

2014-01-01

Equilibrium H/D fractionation factors have been extensively employed to qualitatively assess hydrogen bond strengths in protein structure, enzyme active sites, and DNA. It remains unclear how fractionation factors correlate with hydrogen bond free energies, however. Here we develop an empirical relationship between fractionation factors and free energy, allowing for the simple and quantitative measurement of hydrogen bond free energies. Applying our empirical relationship to prior fractionation factor studies in proteins, we find: [1] Within the folded state, backbone hydrogen bonds are only marginally stronger on average in α-helices compared to β-sheets by ∼0.2 kcal/mol. [2] Charge-stabilized hydrogen bonds are stronger than neutral hydrogen bonds by ∼2 kcal/mol on average, and can be as strong as –7 kcal/mol. [3] Changes in a few hydrogen bonds during an enzyme catalytic cycle can stabilize an intermediate state by –4.2 kcal/mol. [4] Backbone hydrogen bonds can make a large overall contribution to the energetics of conformational changes, possibly playing an important role in directing conformational changes. [5] Backbone hydrogen bonding becomes more uniform overall upon ligand binding, which may facilitate participation of the entire protein structure in events at the active site. Our energetic scale provides a simple method for further exploration of hydrogen bond free energies. PMID:24501090

Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules.

PubMed

Ayoub, Ahmed T; Craddock, Travis J A; Klobukowski, Mariusz; Tuszynski, Jack

2014-08-05

Microtubules are key structural elements that, among numerous biological functions, maintain the cytoskeleton of the cell and have a major role in cell division, which makes them important cancer chemotherapy targets. Understanding the energy balance that brings tubulin dimers, the building blocks of microtubules, together to form a microtubule is especially important for revealing the mechanism of their dynamic instability. Several studies have been conducted to estimate various contributions to the free energy of microtubule formation. However, the hydrogen-bond contribution was not studied before as a separate component. In this work, we use concepts such as the quantum theory of atoms in molecules to estimate the per-residue strength of hydrogen bonds contributing to the overall stability that brings subunits together in pair of tubulin heterodimers, across both the longitudinal and lateral interfaces. Our study shows that hydrogen bonding plays a major role in the stability of tubulin systems. Several residues that are crucial to the binding of vinca alkaloids are shown to be strongly involved in longitudinal microtubule stabilization. This indicates a direct relation between the binding of these agents and the effect on the interfacial hydrogen-bonding network, and explains the mechanism of their action. Lateral contacts showed much higher stability than longitudinal ones (-462 ± 70 vs. -392 ± 59 kJ/mol), which suggests a dramatic lateral stabilization effect of the GTP cap in the β-subunit. The role of the M-loop in lateral stability in absence of taxol was shown to be minor. The B-lattice lateral hydrogen bonds are shown to be comparable in strength to the A-lattice ones (-462 ± 70 vs. -472 ± 46 kJ/mol). These findings establish the importance of hydrogen bonds to the stability of tubulin systems. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs

NASA Astrophysics Data System (ADS)

Böhm, Hans-Joachim

1998-07-01

A dataset of 82 protein-ligand complexes of known 3D structure and binding constant Ki was analysed to elucidate the important factors that determine the strength of protein-ligand interactions. The following parameters were investigated: the number and geometry of hydrogen bonds and ionic interactions between the protein and the ligand, the size of the lipophilic contact surface, the flexibility of the ligand, the electrostatic potential in the binding site, water molecules in the binding site, cavities along the protein-ligand interface and specific interactions between aromatic rings. Based on these parameters, a new empirical scoring function is presented that estimates the free energy of binding for a protein-ligand complex of known 3D structure. The function distinguishes between buried and solvent accessible hydrogen bonds. It tolerates deviations in the hydrogen bond geometry of up to 0.25 Å in the length and up to 30 °Cs in the hydrogen bond angle without penalizing the score. The new energy function reproduces the binding constants (ranging from 3.7 × 10-2 M to 1 × 10-14 M, corresponding to binding energies between -8 and -80 kJ/mol) of the dataset with a standard deviation of 7.3 kJ/mol corresponding to 1.3 orders of magnitude in binding affinity. The function can be evaluated very fast and is therefore also suitable for the application in a 3D database search or de novo ligand design program such as LUDI. The physical significance of the individual contributions is discussed.

A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds.

PubMed

Wang, Changwei; Danovich, David; Shaik, Sason; Mo, Yirong

2017-04-11

Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i.e., hyperconjugation in bonding systems) has been regarded as one of the key forces, it would be illuminating to compare the structures and vibrational frequencies in bonding complexes with the charge transfer effect "turned on" and "turned off". Turning off the charge transfer mixing can be achieved by employing the block-localized wave function (BLW) method, which is an ab initio valence bond (VB) method. Further, with the BLW method, the overall stability gained in the formation of a complex can be analyzed in terms of a few physically meaningful terms. Thus, the BLW method provides a unified and physically lucid way to explore the nature of red- and blue-shifting phenomena in both hydrogen and halogen bonding complexes. In this study, a direct correlation between the total stability and the variation of the Y-A bond length is established based on our BLW computations, and the consistent roles of all energy components are clarified. The n(D) → σ*(Y-A) electron transfer stretches the Y-A bond, while the polarization due to the approach of interacting moieties reduces the HOMO-LUMO gap and results in a stronger orbital mixing within the YA monomer. As a consequence, both the charge transfer and polarization stabilize bonding systems with the Y-A bond stretched and red-shift the vibrational frequency of the Y-A bond. Notably, the energy of the frozen wave function is the only energy component which prefers the shrinking of the Y-A bond and thus is responsible for the associated blue-shifting. The total variations of the Y-A bond length and the corresponding stretching vibrational frequency are thus determined by the competition between the frozen-energy term and the sum of polarization and charge transfer energy terms. Because the frozen energy is composed of electrostatic and Pauli exchange interactions and frequency shifting is a long-range phenomenon, we conclude that long-range electrostatic interaction is the driving force behind the frozen energy term.

Theoretical study of hydrogen bond interactions of fluvastatin with ι-carrageenan and λ-carrageenan.

PubMed

Papadopoulos, Anastasios G; Sigalas, Michael P

2011-07-01

The binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug's release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three low energy conformers of fluvastatin have been calculated. The vibrational spectroscopic properties calculated for the most stable conformer were in satisfactory agreement with the experimental data. A series of hydrogen bonded complexes of the most stable conformer of fluvastatin anion with low molecular weight models of the polymers have been fully optimized. In almost all, intermolecular H-bonds are formed between the sulfate groups of ι- or λ-carrageenan and fluvastatin's hydroxyls, resulting in a red shift of the fluvastatin's O - H stretching vibrations. Cooperative intramolecular H-bonds within fluvastatin or ι-, λ-carrageenan are also present. The BSSE and ZPE corrected interaction energies were estimated in the range 281-318 kJ mol⁻¹ for ι-carrageenan - fluvastatin and 145-200 kJ mol⁻¹ for λ-carrageenan - fluvastatin complexes. The electron density (ρ (bcp)) and Laplacian (∇²ρ (bcp)) properties at critical points of the intermolecular hydrogen bonds, estimated by AIM (atoms in molecules) calculations, have a low and positive character (∇²ρ(bcp) > 0), consistent with the electrostatic character of the hydrogen bonds. The structural and energetic data observed, as well as the extent of the red shift of the fluvastatin's O - H stretching vibrations upon complex formation and the properties of electron density show a stronger binding of fluvastatin to ι- than to λ-carrageenan.

Chemoselective Aliphatic C–H Bond Oxidation Enabled by Polarity Reversal

PubMed Central

2017-01-01

Methods for selective oxidation of aliphatic C–H bonds are called on to revolutionize organic synthesis by providing novel and more efficient paths. Realization of this goal requires the discovery of mechanisms that can alter in a predictable manner the innate reactivity of these bonds. Ideally, these mechanisms need to make oxidation of aliphatic C–H bonds, which are recognized as relatively inert, compatible with the presence of electron rich functional groups that are highly susceptible to oxidation. Furthermore, predictable modification of the relative reactivity of different C–H bonds within a molecule would enable rapid diversification of the resulting oxidation products. Herein we show that by engaging in hydrogen bonding, fluorinated alcohols exert a polarity reversal on electron rich functional groups, directing iron and manganese catalyzed oxidation toward a priori stronger and unactivated C–H bonds. As a result, selective hydroxylation of methylenic sites in hydrocarbons and remote aliphatic C–H oxidation of otherwise sensitive alcohol, ether, amide, and amine substrates is achieved employing aqueous hydrogen peroxide as oxidant. Oxidations occur in a predictable manner, with outstanding levels of product chemoselectivity, preserving the first-formed hydroxylation product, thus representing an extremely valuable tool for synthetic planning and development. PMID:29296677

Chemoselective Aliphatic C-H Bond Oxidation Enabled by Polarity Reversal.

PubMed

Dantignana, Valeria; Milan, Michela; Cussó, Olaf; Company, Anna; Bietti, Massimo; Costas, Miquel

2017-12-27

Methods for selective oxidation of aliphatic C-H bonds are called on to revolutionize organic synthesis by providing novel and more efficient paths. Realization of this goal requires the discovery of mechanisms that can alter in a predictable manner the innate reactivity of these bonds. Ideally, these mechanisms need to make oxidation of aliphatic C-H bonds, which are recognized as relatively inert, compatible with the presence of electron rich functional groups that are highly susceptible to oxidation. Furthermore, predictable modification of the relative reactivity of different C-H bonds within a molecule would enable rapid diversification of the resulting oxidation products. Herein we show that by engaging in hydrogen bonding, fluorinated alcohols exert a polarity reversal on electron rich functional groups, directing iron and manganese catalyzed oxidation toward a priori stronger and unactivated C-H bonds. As a result, selective hydroxylation of methylenic sites in hydrocarbons and remote aliphatic C-H oxidation of otherwise sensitive alcohol, ether, amide, and amine substrates is achieved employing aqueous hydrogen peroxide as oxidant. Oxidations occur in a predictable manner, with outstanding levels of product chemoselectivity, preserving the first-formed hydroxylation product, thus representing an extremely valuable tool for synthetic planning and development.

Influence of Hydrogen Bonding on the Surface Diffusion of Molecular Glasses: Comparison of Three Triazines

DOE PAGES

Chen, Yinshan; Zhu, Men; Laventure, Audrey; ...

2017-06-26

Surface grating decay measurements have been performed on three closely related molecular glasses to study the effect of intermolecular hydrogen bonds on surface diffusion. The three molecules are derivatives of bis(3,5-dimethyl-phenylamino)-1,3,5-triazine and differ only in the functional group R at the 2-position, with R being C 2H 5, OCH 3, and NHCH 3, and referred to as “Et”, “OMe”, and “NHMe”, respectively. Of the three molecules, NHMe forms more extensive intermolecular hydrogen bonds than Et and OMe and was found to have slower surface diffusion. For Et and OMe, surface diffusion is so fast that it replaces viscous flow asmore » the mechanism of surface grating decay as temperature is lowered. In contrast, no such transition was observed for NHMe under the same conditions, indicating significantly slower surface diffusion. This result is consistent with the previous finding that extensive intermolecular hydrogen bonds slow down surface diffusion in molecular glasses and is attributed to the persistence of hydrogen bonds even in the surface environment. Here, this result is also consistent with the lower stability of the vapor-deposited glass of NHMe relative to those of Et and OMe and supports the view that surface mobility controls the stability of vapor-deposited glasses.« less

Structural elements of the signal propagation pathway in squid rhodopsin and bovine rhodopsin.

PubMed

Sugihara, Minoru; Fujibuchi, Wataru; Suwa, Makiko

2011-05-19

Squid and bovine rhodopsins are G-protein coupled receptors (GPCRs) that activate Gq- and Gt-type G-proteins, respectively. To understand the structural elements of the signal propagation pathway, we performed molecular dynamics (MD) simulations of squid and bovine rhodopsins plus a detailed sequence analysis of class A GPCRs. The computations indicate that although the geometry of the retinal is similar in bovine and squid rhodopsins, the important interhelical hydrogen bond networks are different. In squid rhodopsin, an extended hydrogen bond network that spans ∼13 Å to Tyr315 on the cytoplasmic site is present regardless of the protonation state of Asp80. In contrast, the extended hydrogen bond network is interrupted at Tyr306 in bovine rhodopsin. Those differences in the hydrogen bond network may play significant functional roles in the signal propagation from the retinal binding site to the cytoplasmic site, including transmembrane helix (TM) 6 to which the G-protein binds. The MD calculations demonstrate that the elongated conformation of TM6 in squid rhodopsin is stabilized by salt bridges formed with helix (H) 9. Together with the interhelical hydrogen bonds, the salt bridges between TM6 and H9 stabilize the protein conformation of squid rhodopsin and may hinder the occurrence of large conformational changes that are observed upon activation of bovine rhodopsin. © 2011 American Chemical Society

Exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from Thermus thermophilus

PubMed Central

Chang, Hsin-Yang; Choi, Sylvia K.; Vakkasoglu, Ahmet Selim; Chen, Ying; Hemp, James; Fee, James A.; Gennis, Robert B.

2012-01-01

The heme-copper oxygen reductases are redox-driven proton pumps. In the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba3-type oxygen reductase from Thermus thermophilus, leading from the propionates of heme a3 to the interface between subunits I and II. Recent studies have proposed important roles for His376 and Asp372, both of which are hydrogen-bonded to propionate-A of heme a3, and for Glu126II (subunit II), which is hydrogen-bonded to His376. Based on the current results, His376, Glu126II, and Asp372 are not essential for either oxidase activity or proton pumping. In addition, Tyr133, which is hydrogen-bonded to propionate-D of heme a3, was also shown not to be essential for function. However, two mutations of the residues hydrogen-bonded to propionate-A, Asp372Ile and His376Asn, retain high electron transfer activity and normal spectral features but, in different preparations, either do not pump protons or exhibit substantially diminished proton pumping. It is concluded that either propionate-A of heme a3 or possibly the cluster of groups centered about the conserved water molecule that hydrogen-bonds to both propionates-A and -D of heme a3 is a good candidate to be the proton loading site. PMID:22431640

Exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from Thermus thermophilus.

PubMed

Chang, Hsin-Yang; Choi, Sylvia K; Vakkasoglu, Ahmet Selim; Chen, Ying; Hemp, James; Fee, James A; Gennis, Robert B

2012-04-03

The heme-copper oxygen reductases are redox-driven proton pumps. In the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba(3)-type oxygen reductase from Thermus thermophilus, leading from the propionates of heme a(3) to the interface between subunits I and II. Recent studies have proposed important roles for His376 and Asp372, both of which are hydrogen-bonded to propionate-A of heme a(3), and for Glu126(II) (subunit II), which is hydrogen-bonded to His376. Based on the current results, His376, Glu126(II), and Asp372 are not essential for either oxidase activity or proton pumping. In addition, Tyr133, which is hydrogen-bonded to propionate-D of heme a(3), was also shown not to be essential for function. However, two mutations of the residues hydrogen-bonded to propionate-A, Asp372Ile and His376Asn, retain high electron transfer activity and normal spectral features but, in different preparations, either do not pump protons or exhibit substantially diminished proton pumping. It is concluded that either propionate-A of heme a(3) or possibly the cluster of groups centered about the conserved water molecule that hydrogen-bonds to both propionates-A and -D of heme a(3) is a good candidate to be the proton loading site.

Tetraalkylammonium Salts as Hydrogen-Bonding Catalysts.

PubMed

Shirakawa, Seiji; Liu, Shiyao; Kaneko, Shiho; Kumatabara, Yusuke; Fukuda, Airi; Omagari, Yumi; Maruoka, Keiji

2015-12-21

Although the hydrogen-bonding ability of the α hydrogen atoms on tetraalkylammonium salts is often discussed with respect to phase-transfer catalysts, catalysis that utilizes the hydrogen-bond-donor properties of tetraalkylammonium salts remains unknown. Herein, we demonstrate hydrogen-bonding catalysis with newly designed tetraalkylammonium salt catalysts in Mannich-type reactions. The structure and the hydrogen-bonding ability of the new ammonium salts were investigated by X-ray diffraction analysis and NMR titration studies. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanistic aspects of hydrogen abstraction for phenolic antioxidants. Electronic structure and topological electron density analysis.

PubMed

Singh, Nakul; O'Malley, Patrick J; Popelier, Paul L A

2005-02-21

Density functional calculations using the B3LYP functional are used to provide insight into the hydrogen abstraction mechanism of phenolic antioxidants. The energy profiles for 13 ortho, meta, para and di-methyl substituted phenols with hydroperoxyl radical have been determined. An excellent correlation between the enthalpy (DeltaH) and activation energy (DeltaEa) was found, obeying the Evans-Polanyi rule. The effects of hydrogen bonding on DeltaEa are also discussed. Electron donating groups at the ortho and para positions are able to lower the activation energy for hydrogen abstraction. The highly electron withdrawing fluoro substituent increases the activation energies relative to phenol at the meta position but not at the para position. The electron density is studied using the atoms in molecules (AIM) approach. Atomic and bond properties are extracted to describe the hydrogen atom abstraction mechanism. It is found that on going from reactants to transition state, the hydrogen atom experiences a loss in volume, electronic population and dipole moment. These features suggest that the phenol hydroperoxyl reactions proceed according to a proton coupled electron transfer (PCET) as opposed to a hydrogen atom transfer (HAT) mechanism.

Structural analysis of phospholipase A2 from functional perspective. 1. Functionally relevant solution structure and roles of the hydrogen-bonding network.

PubMed

Yuan, C; Byeon, I J; Li, Y; Tsai, M D

1999-03-09

Bovine pancreatic phospholipase A2 (PLA2), a small (13.8 kDa) Ca2+-dependent lipolytic enzyme, is rich in functional and structural character. In an effort to examine its detailed structure-function relationship, we determined its solution structure by multidimensional nuclear magnetic resonance (NMR) spectroscopy at a functionally relevant pH. An ensemble of 20 structures generated has an average root-mean-square deviation (RMSD) of 0.62 +/- 0.08 A for backbone (N, Calpha, C) atoms and 0.98 +/- 0.09 A for all heavy atoms. The overall structure shows several notable differences from the crystal structure: the first three residues at the N-terminus, the calcium-binding loop (Y25-T36), and the surface loop (V63-N72) appear to be flexible; the alpha-helical conformation of helix B (E17-F22) is absent; helix D appears to be shorter (D59-V63 instead of D59-D66); and the hydrogen-bonding network is less defined. These differences were analyzed in relation to the function of PLA2. We then further examined the H-bonding network, because its functional role or even its existence in solution has been in dispute recently. Our results show that part of the H-bonding network (the portion away from N-terminus) clearly exists in solution, as evidenced by direct observation (at 11.1 ppm) of a strong H-bond between Y73 and D99 and an implicated interaction between D99 and H48. Analyses of a series of mutants indicated that the existence of the Y73.D99 H-bond correlates directly with the conformational stability of the mutant. Loss of this H-bond results in a loss of 2-3 kcal/mol in the conformational stability of PLA2. The unequivocal identification and demonstration of the structural importance of a specific hydrogen bond, and the magnitude of its contribution to conformational stability, are uncommon to the best of our knowledge. Our results also suggest that, while the D99.H48 catalytic diad is the key catalytic machinery of PLA2, it also helps to maintain conformational integrity.

A theoretical study of hydrogen complexes of the XH-pi type between propyne and HF, HCL or HCN.

PubMed

Tavares, Alessandra M; da Silva, Washington L V; Lopes, Kelson C; Ventura, Elizete; Araújo, Regiane C M U; do Monte, Silmar A; da Silva, João Bosco P; Ramos, Mozart N

2006-05-15

The present manuscript reports a systematic investigation of the basis set dependence of some properties of hydrogen-bonded (pi type) complexes formed by propyne and a HX molecule, where X=F, Cl and CN. The calculations have been performed at Hartree-Fock, MP2 and B3LYP levels. Geometries, H-bond energies and vibrational have been considered. The more pronounced effects on the structural parameters of the isolated molecules, as a result of complexation, are verified on RCtriple bondC and HX bond lengths. As compared to double-zeta (6-31G**), triple-zeta (6-311G**) basis set leads to an increase of RCtriple bondC bond distance, at all three computational levels. In the case where diffuse functions are added to both hydrogen and 'heavy' atoms, the effect is more pronounced. The propyne-HX structural parameters are quite similar to the corresponding parameters of acetylene-HX complexes, at all levels. The largest difference is obtained for hydrogen bond distance, RH, with a smaller value for propyne-HX complex, indicating a stronger bond. Concerning the electronic properties, the results yield the following ordering for H-bond energies, DeltaE: propynecdots, three dots, centeredHF>propynecdots, three dots, centeredHCl>propynecdots, three dots, centeredHCN. It is also important to point out that the inclusion of BSSE and zero-point energies (ZPE) corrections cause significant changes on DeltaE. The smaller effect of ZPE is obtained for propynecdots, three dots, centeredHCN at HF/6-311++G** level, while the greatest difference is obtained at MP2/6-31G** level for propynecdots, three dots, centeredHF system. Concerning the IR vibrational it was obtained that larger shift can be associated with stronger hydrogen bonds. The more pronounced effect on the normal modes of the isolated molecule after the complexation is obtained for HX stretching frequency, which is shifted downward.

Boron nitride nanotube as a delivery system for platinum drugs: Drug encapsulation and diffusion coefficient prediction.

PubMed

Khatti, Zahra; Hashemianzadeh, Seyed Majid

2016-06-10

Molecular dynamics (MD) simulation has been applied to investigate a drug delivery system based on boron nitride nanotubes, particularly the delivery of platinum-based anticancer drugs. For this propose, the behavior of carboplatin drugs inserted in boron nitride nanotubes (BNNT) as a carrier was studied. The diffusion rate of water molecules and carboplatin was investigated inside functionalized and pristine boron nitride nanotubes. The penetration rate of water and drug in functionalized BNNT was higher than that in pristine BNNT due to favorable water-mediated hydrogen bonding in hydroxyl edge-functionalized BNNT. Additionally, the encapsulation of multiple carboplatin drugs inside functionalized boron nitride nanotubes with one to five drug molecules confined inside the nanotube cavity was examined. At high drug loading, the hydrogen bond formation between adjacent drugs and the non-bonded van der Waals interaction between carboplatin and functionalized BNNT inner surface were found to be influential in drug displacement within the functionalized BNNT cavity for higher drug-loading capacity. Copyright © 2016 Elsevier B.V. All rights reserved.

Selective Nitrate Recognition by a Halogen‐Bonding Four‐Station [3]Rotaxane Molecular Shuttle

PubMed Central

Barendt, Timothy A.; Docker, Andrew; Marques, Igor; Félix, Vítor

2016-01-01

Abstract The synthesis of the first halogen bonding [3]rotaxane host system containing a bis‐iodo triazolium‐bis‐naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo‐triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion–rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the 1H NMR anion binding results. PMID:27436297

Hydrogen-bonding Interactions between Apigenin and Ethanol/Water: A Theoretical Study

NASA Astrophysics Data System (ADS)

Zheng, Yan-Zhen; Zhou, Yu; Liang, Qin; Chen, Da-Fu; Guo, Rui; Lai, Rong-Cai

2016-10-01

In this work, hydrogen-bonding interactions between apigenin and water/ethanol were investigated from a theoretical perspective using quantum chemical calculations. Two conformations of apigenin molecule were considered in this work. The following results were found. (1) For apigenin monomer, the molecular structure is non-planar, and all of the hydrogen and oxygen atoms can be hydrogen-bonding sites. (2) Eight and seven optimized geometries are obtained for apigenin (I)-H2O/CH3CH2OH and apigenin (II)-H2O/CH3CH2OH complexes, respectively. In apigenin, excluding the aromatic hydrogen atoms in the phenyl substituent, all other hydrogen atoms and the oxygen atoms form hydrogen-bonds with H2O and CH3CH2OH. (3) In apigenin-H2O/CH3CH2OH complexes, the electron density and the E(2) in the related localized anti-bonding orbital are increased upon hydrogen-bond formation. These are the cause of the elongation and red-shift of the X-H bond. The sum of the charge change transfers from the hydrogen-bond acceptor to donor. The stronger interaction makes the charge change more intense than in the less stable structures. (4) Most of the hydrogen-bonds in the complexes are electrostatic in nature. However, the C4-O5···H, C9-O4···H and C13-O2···H hydrogen-bonds have some degree of covalent character. Furthermore, the hydroxyl groups of the apigenin molecule are the preferred hydrogen-bonding sites.

DOE Office of Scientific and Technical Information (OSTI.GOV)

San Fabián, J.; Omar, S.; García de la Vega, J. M., E-mail: garcia.delavega@uam.es

The effect of a fraction of Hartree-Fock exchange on the calculated spin-spin coupling constants involving fluorine through a hydrogen bond is analyzed in detail. Coupling constants calculated using wavefunction methods are revisited in order to get high-level calculations using the same basis set. Accurate MCSCF results are obtained using an additive approach. These constants and their contributions are used as a reference for density functional calculations. Within the density functional theory, the Hartree-Fock exchange functional is split in short- and long-range using a modified version of the Coulomb-attenuating method with the SLYP functional as well as with the original B3LYP.more » Results support the difficulties for calculating hydrogen bond coupling constants using density functional methods when fluorine nuclei are involved. Coupling constants are very sensitive to the Hartree-Fock exchange and it seems that, contrary to other properties, it is important to include this exchange for short-range interactions. Best functionals are tested in two different groups of complexes: those related with anionic clusters of type [F(HF){sub n}]{sup −} and those formed by difluoroacetylene and either one or two hydrogen fluoride molecules.« less

Structure and stability of complexes of agmatine with some functional receptor residues of proteins

NASA Astrophysics Data System (ADS)

Remko, Milan; Broer, Ria; Remková, Anna; Van Duijnen, Piet Th.

2017-04-01

The paper reports the results of a theoretical study of the conformational behavior and basicity of biogenic amine agmatine. The complexes modelling of agmatine - protein interaction are also under scrutiny of our investigation using the Becke3LYP and B97D levels of the density functional theory. The relative stabilities (Gibbs energies) of individual complexes are by both DFT methods described equally. Hydration has a dramatic effect on the hydrogen bonded complexes studied. The pairing acidic carboxylate group with different agmatine species resulted in charged hydrogen bond complexes containing negatively charged acetate species acting as proton acceptors.

Economical and accurate protocol for calculating hydrogen-bond-acceptor strengths.

PubMed

El Kerdawy, Ahmed; Tautermann, Christofer S; Clark, Timothy; Fox, Thomas

2013-12-23

A series of density functional/basis set combinations and second-order Møller-Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques.

Intramolecular hydrogen bonds: ab initio Car Parrinello simulations of arylamide torsions

NASA Astrophysics Data System (ADS)

Doerksen, Robert J.; Chen, Bin; Klein, Michael L.

2003-10-01

Gas-phase, room temperature Car-Parrinello molecular dynamics simulations using the HCTH density functional are reported for the arylamides acetanilide ( 1) and ortho-methylthioacetanilide ( 2). The simulations show that in 1, rotation around the ring-amide bond is relatively unrestricted. By contrast, in 2 the methylthio side chain encourages the amide to be directed with N-H pointing toward S, not to flip by 360°, and furthermore to remain close to coplanar with the benzene ring. Because of an intramolecular N-H⋯S hydrogen bond, the N-H stretch frequency of 2 is red-shifted by ˜78 cm -1 compared to that of 1.

Laser spectroscopic visualization of hydrogen bond motions in liquid water

NASA Astrophysics Data System (ADS)

Bratos, S.; Leicknam, J.-Cl.; Pommeret, S.; Gallot, G.

2004-12-01

Ultrafast pump-probe experiments are described permitting a visualization of molecular motions in diluted HDO/D 2O solutions. The experiments were realized in the mid-infrared spectral region with a time resolution of 150 fs. They were interpreted by a careful theoretical analysis, based on the correlation function approach of statistical mechanics. Combining experiment and theory, stretching motions of the OH⋯O bonds as well as HDO rotations were 'filmed' in real time. It was found that molecular rotations are the principal agent of hydrogen bond breaking and making in water. Recent literatures covering the subject, including molecular dynamics simulations, are reviewed in detail.

Spiroacetal formation through telescoped cycloaddition and carbon-hydrogen bond functionalization: total synthesis of bistramide A.

PubMed

Han, Xun; Floreancig, Paul E

2014-10-06

Spiroacetals can be formed through a one-pot sequence of a hetero-Diels-Alder reaction, an oxidative carbon-hydrogen bond cleavage, and an acid treatment. This convergent approach expedites access to a complex molecular subunit which is present in numerous biologically active structures. The utility of the protocol is demonstrated through its application to a brief synthesis of the actin-binding cytotoxin bistramide A. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Anodic Oxidative Modification of Egg White for Heat Treatment.

PubMed

Takahashi, Masahito; Handa, Akihiro; Yamaguchi, Yusuke; Kodama, Risa; Chiba, Kazuhiro

2016-08-31

A new functionalization of egg white was achieved by an electrochemical reaction. The method involves electron transfer from thiol groups of egg white protein to form disulfide bonds. The oxidized egg white produced less hydrogen sulfide during heat treatment; with sufficient application of electricity, almost no hydrogen sulfide was produced. In addition, gels formed by heating electrochemically oxidized egg white exhibited unique properties, such as a lower gelation temperature and a softened texture, presumably due to protein aggregation and electrochemically mediated intramolecular disulfide bond formation.

Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters.

PubMed

Yang, Zhong-Zhi; Wu, Yang; Zhao, Dong-Xia

2004-02-08

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces "the hydrogen bond interaction region" in which a new parameter k(lp,H)(R(lp,H)) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom-atom interaction, i.e., oxygen-oxygen, hydrogen-hydrogen, oxygen-hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H(2)O)(n) (n=2-6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems.

The influence of hydrogen bonding on partition coefficients

NASA Astrophysics Data System (ADS)

Borges, Nádia Melo; Kenny, Peter W.; Montanari, Carlos A.; Prokopczyk, Igor M.; Ribeiro, Jean F. R.; Rocha, Josmar R.; Sartori, Geraldo Rodrigues

2017-02-01

This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect `frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.

Hydroperoxides as Hydrogen Bond Donors

NASA Astrophysics Data System (ADS)

Møller, Kristian H.; Tram, Camilla M.; Hansen, Anne S.; Kjaergaard, Henrik G.

2016-06-01

Hydroperoxides are formed in the atmosphere following autooxidation of a wide variety of volatile organics emitted from both natural and anthropogenic sources. This raises the question of whether they can form hydrogen bonds that facilitate aerosol formation and growth. Using a combination of Fourier transform infrared spectroscopy, FT-IR, and ab initio calculations, we have compared the gas phase hydrogen bonding ability of tert-butylhydroperoxide (tBuOOH) to that of tert-butanol (tBuOH) for a series of bimolecular complexes with different acceptors. The hydrogen bond acceptor atoms studied are nitrogen, oxygen, phosphorus and sulphur. Both in terms of calculated redshifts and binding energies (BE), our results suggest that hydroperoxides are better hydrogen bond donors than the corresponding alcohols. In terms of hydrogen bond acceptor ability, we find that nitrogen is a significantly better acceptor than the other three atoms, which are of similar strength. We observe a similar trend in hydrogen bond acceptor ability with other hydrogen bond donors including methanol and dimethylamine.

Aggregation of nitroaniline in tetrahydrofuran through intriguing H-bond formation by sodium borohydride.

PubMed

Ganguly, Mainak; Mondal, Chanchal; Pal, Anjali; Pratik, Saied Md; Pal, Jaya; Pal, Tarasankar

2014-07-07

The participation of sodium borohydride (NaBH4) in hydrogen bonding interactions and transient anion radical formation has been proved. Thus, the properties of NaBH4 are extended beyond the purview of its normal reducing capability and nucleophilic property. It is reported that ortho- and para-nitroanilines (NAs) form stable aggregates only in tetrahydrofuran (THF) in the presence of NaBH4 and unprecedented orange/red colorations are observed. The same recipe with nitrobenzene instead of nitroanilines (NAs) in the presence of NaBH4 evolves a transient rose red solution due to the formation of a highly fluorescent anion radical. Spectroscopic studies (UV-vis, fluorescence, RLS, Raman, NMR etc.) as well as theoretical calculations supplement the J-aggregate formation of NAs due to extensive hydrogen bonding. This is the first report where BH4(-) in THF has been shown to support such an aggregation process through H-bonding. It is further confirmed that stable intermolecular hydrogen bond-induced aggregation requires a geometrical match in both the nitro- and amino-functionalities attached to the phenyl ring with proper geometry. On the contrary, meta-nitroaniline remains as the odd man out and does not take part in such aggregation. Surprisingly, Au nanoparticles dismantle the J-aggregates of NA in THF. Explicit hydrogen bond formation in NA has been confirmed experimentally considering its promising applications in different fields including non-linear optics.

Functional organic materials based on polymerized liquid-crystal monomers: supramolecular hydrogen-bonded systems.

PubMed

Broer, Dirk J; Bastiaansen, Cees M W; Debije, Michael G; Schenning, Albertus P H J

2012-07-16

Functional organic materials are of great interest for a variety of applications. To obtain precise functional properties, well-defined hierarchically ordered supramolecular materials are crucial. The self-assembly of liquid crystals has proven to be an extremely useful tool in the development of well-defined nanostructured materials. We have chosen the illustrative example of photopolymerizable hydrogen-bonding mesogens to show that a wide variety of functional materials can be made from a relatively simple set of building blocks. Upon mixing these compounds with other reactive mesogens, nematic, chiral nematic, and smectic or columnar liquid-crystalline phases can be formed that can be applied as actuators, sensors and responsive reflectors, and nanoporous membranes, respectively. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influence of intermolecular amide hydrogen bonding on the geometry, atomic charges, and spectral modes of acetanilide: An ab initio study

NASA Astrophysics Data System (ADS)

Binoy, J.; Prathima, N. B.; Murali Krishna, C.; Santhosh, C.; Hubert Joe, I.; Jayakumar, V. S.

2006-08-01

Acetanilide, a compound of pharmaceutical importance possessing pain-relieving properties due to its blocking the pulse dissipating along the nerve fiber, is subjected to vibrational spectral investigation using NIR FT Raman, FT-IR, and SERS. The geometry, Mulliken charges, and vibrational spectrum of acetanilide have been computed using the Hartree-Fock theory and density functional theory employing the 6-31G (d) basis set. To investigate the influence of intermolecular amide hydrogen bonding, the geometry, charge distribution, and vibrational spectrum of the acetanilide dimer have been computed at the HF/6-31G (d) level. The computed geometries reveal that the acetanilide molecule is planar, while twisting of the secondary amide group with respect to the phenyl ring is found upon hydrogen bonding. The trans isomerism and “amido” form of the secondary amide, hyperconjugation of the C=O group with the adjacent C-C bond, and donor-acceptor interaction have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of the phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation, and hyperconjugation. A decrease in the NH and C=O bond orders and increase in the C-N bond orders due to donor-acceptor interaction can be observed in the vibrational spectra. The SERS spectral analysis reveals that the flat orientation of the molecule on the adsorption plane is preferred.

Hydrogen bonds of sodium alginate/Antarctic krill protein composite material.

PubMed

Yang, Lijun; Guo, Jing; Yu, Yue; An, Qingda; Wang, Liyan; Li, Shenglin; Huang, Xuelin; Mu, Siyang; Qi, Shanwei

2016-05-20

Sodium alginate/Antarctic krill protein composite material (SA/AKP) was successfully obtained by blending method. The hydrogen bonds of SA/AKP composite material were analyzed by Fourier transform infrared spectroscopy (FT-IR) and Nuclear magnetic resonance hydrogen spectrum (HNMR). Experiment manifested the existence of intermolecular and intramolecular hydrogen bonds in SA/AKP system; strength of intermolecular hydrogen bond enhanced with the increase of AKP in the composite material and the interaction strength of hydrogen bonding followed the order: OH…Ether O>OH…π>OH…N. The percentage of intermolecular hydrogen bond decreased with increase of pH. At the same time, the effect of hydrogen bonds on properties of the composite material was discussed. The increase of intermolecular hydrogen bonding led to the decrease of crystallinity, increase of apparent viscosity and surface tension, as well as obvious decrease of heat resistance of SA/AKP composite material. SA/AKP fiber SEM images and energy spectrum showed that crystallized salt was separated from the fiber, which possibly led to the fibrillation of the composite fibers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Polymer sol-gel composite inverse opal structures.

PubMed

Zhang, Xiaoran; Blanchard, G J

2015-03-25

We report on the formation of composite inverse opal structures where the matrix used to form the inverse opal contains both silica, formed using sol-gel chemistry, and poly(ethylene glycol), PEG. We find that the morphology of the inverse opal structure depends on both the amount of PEG incorporated into the matrix and its molecular weight. The extent of organization in the inverse opal structure, which is characterized by scanning electron microscopy and optical reflectance data, is mediated by the chemical bonding interactions between the silica and PEG constituents in the hybrid matrix. Both polymer chain terminus Si-O-C bonding and hydrogen bonding between the polymer backbone oxygens and silanol functionalities can contribute, with the polymer mediating the extent to which Si-O-Si bonds can form within the silica regions of the matrix due to hydrogen-bonding interactions.

The CH/π hydrogen bond: Implication in chemistry

NASA Astrophysics Data System (ADS)

Nishio, M.

2012-06-01

The CH/π hydrogen bond is the weakest extreme of hydrogen bonds that occurs between a soft acid CH and a soft base π-system. Implication in chemistry of the CH/π hydrogen bond includes issues of conformation, crystal packing, and specificity in host/guest complexes. The result obtained by analyzing the Cambridge Structural Database is reviewed. The peculiar axial preference of isopropyl group in α-phellandrene and folded conformation of levopimaric acid have been explained in terms of the CH/π hydrogen bond, by high-level ab initio MO calculations. Implication of the CH/π hydrogen bond in structural biology is also discussed, briefly.

Engineering solid-state materials. Strategies for modeling and packing control of molecular assemblies into 3-D networks

NASA Astrophysics Data System (ADS)

Videnova-Adrabinska, V.; Etter, M. C.; Ward, M. D.

1993-04-01

The crystal structure and properties of a number of urea cocrystals are studied with regard to symmetry of the hydrogen-bonded molecular assemblies. The logical consequences of hydrogen bonding interactions are followed step-by-step. The problems of aggregate formation, nucleation, and crystal growth are also elucidated. Endeavor is made to envisage the 2-D and 3-D hydrogen bond network in a manageable way by exploiting graph set short hand. Strategies of how to control the symmetry of molecular packing are still to be elaborated. In our strategy, the programmed self-assembly has been based on the principle of molecular recognition of self- and hetero-complementary functional groups. However, the main focus for pre-organizational control has been put on the two-fold axis estimator of the urea molecule.

Evaluating the Energetic Driving Force for Cocrystal Formation

PubMed Central

2017-01-01

We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol–1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems—hydrogen-bonded, halogen-bonded, and weakly bound cocrystals—finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition—more densely packed cocrystals with stronger hydrogen bonding tend to be more stable—but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems. PMID:29445316

Evaluating the Energetic Driving Force for Cocrystal Formation.

PubMed

Taylor, Christopher R; Day, Graeme M

2018-02-07

We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol -1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems-hydrogen-bonded, halogen-bonded, and weakly bound cocrystals-finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition-more densely packed cocrystals with stronger hydrogen bonding tend to be more stable-but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems.

Evans hole and non linear optical activity in Bis(melaminium) sulphate dihydrate: A vibrational spectral study.

PubMed

Suresh Kumar, V R; Binoy, J; Dawn Dharma Roy, S; Marchewka, M K; Jayakumar, V S

2015-01-01

Bis(melaminium) sulphate dihydrate (BMSD), an interesting melaminium derivative for nonlinear optical activity, has been subjected to vibrational spectral analysis using FT IR and FT Raman spectra. The analysis has been aided by the Potential Energy Distribution (PED) of vibrational spectral bands, derived using density functional theory (DFT) at B3LYP/6-31G(d) level. The geometry is found to correlate well with the XRD structure and the band profiles for certain vibrations in the finger print region have been theoretically explained using Evans hole. The detailed Natural Bond Orbital (NBO) analysis of the hydrogen bonding in BMSD has also been carried out to understand the correlation between the stabilization energy of hyperconjugation of the lone pair of donor with the σ(∗) orbital of hydrogen-acceptor bond and the strength of hydrogen bond. The theoretical calculation shows that BMSD has NLO efficiency, 2.66 times that of urea. The frontier molecular orbital analysis points to a charge transfer, which contributes to NLO activity, through N-H…O intermolecular hydrogen bonding between the melaminium ring and the sulphate. The molecular electrostatic potential (MEP) mapping has also been performed for the detailed analysis of the mutual interactions between melaminium ring and sulphate ion. Copyright © 2015 Elsevier B.V. All rights reserved.

Structural and spectroscopic investigation of the N-methylformamide-water (NMF···3H2O) complex

NASA Astrophysics Data System (ADS)

Hammami, F.; Ghalla, H.; Chebaane, A.; Nasr, S.

2015-01-01

In this work, theoretical studies on the structure, molecular properties, hydrogen bonding, and vibrational spectra of the N-methylformamide-water (NMF...3H2O) complex will be presented. The molecular geometry was optimised by using Hartree-Fock (HF), second Møller-Plesset (MP2), and density functional theory methods with different basis sets. The harmonic vibrational frequencies are computed by using the B3LYP method with 6-311++G(d,p) as a basis set and then scaled with a suitable scale factor to yield good coherence with the observed values. The temperature dependence of various thermodynamic functions (heat capacity, entropy, and enthalpy changes) was also studied. A detailed analysis of the nature of the hydrogen bonding, using natural bond orbital (NBO) and topological atoms in molecules theory, has been reported.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol.

PubMed

Zhao, Hailiang; Tang, Shanshan; Xu, Xiang; Du, Lin

2016-12-30

Amides are important atmospheric organic-nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N -methylformamide, N , N -dimethylformamide, acetamide, N -methylacetamide and N , N -dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH-amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O-H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

PubMed Central

Zhao, Hailiang; Tang, Shanshan; Xu, Xiang; Du, Lin

2016-01-01

Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components. PMID:28042825

Ultraslow Phase Transitions in an Anion-Anion Hydrogen-Bonded Ionic Liquid.

PubMed

Faria, Luiz F O; Lima, Thamires A; Ferreira, Fabio F; Ribeiro, Mauro C C

2018-02-15

A Raman spectroscopy study of 1-ethyl-3-methylimidazolium hydrogen sulfate, [C 2 C 1 im][HSO 4 ], as a function of temperature, has been performed to reveal the role played by anion-anion hydrogen bond on the phase transitions of this ionic liquid. Anion-anion hydrogen bonding implies high viscosity, good glass-forming ability, and also moderate fragility of [C 2 C 1 im][HSO 4 ] in comparison with other ionic liquids. Heating [C 2 C 1 im][HSO 4 ] from the glassy phase results in cold crystallization at ∼245 K. A solid-solid transition (crystal I → crystal II) is barely discernible in calorimetric measurements at typical heating rates, but it is clearly revealed by Raman spectroscopy and X-ray diffraction. Raman spectroscopy indicates that crystal I has extended ([HSO 4 ] - ) n chains of hydrogen-bonded anions but crystal II has not. Raman spectra recorded at isothermal condition show the ultraslow dynamics of cold crystallization, solid-solid transition, and continuous melting of [C 2 C 1 im][HSO 4 ]. A brief comparison is also provided between [C 2 C 1 im][HSO 4 ] and [C 4 C 1 im][HSO 4 ], as Raman spectroscopy shows that the latter does not form the crystalline phase with extended anion-anion chains.

HBonanza: A Computer Algorithm for Molecular-Dynamics-Trajectory Hydrogen-Bond Analysis

PubMed Central

Durrant, Jacob D.; McCammon, J. Andrew

2011-01-01

In the current work, we present a hydrogen-bond analysis of 2,673 ligand-receptor complexes that suggests the total number of hydrogen bonds formed between a ligand and its protein receptor is a poor predictor of ligand potency; furthermore, even that poor prediction does not suggest a statistically significant correlation between hydrogen-bond formation and potency. While we are not the first to suggest that hydrogen bonds on average do not generally contribute to ligand binding affinities, this additional evidence is nevertheless interesting. The primary role of hydrogen bonds may instead be to ensure specificity, to correctly position the ligand within the active site, and to hold the protein active site in a ligand-friendly conformation. We also present a new computer program called HBonanza (hydrogen-bond analyzer) that aids the analysis and visualization of hydrogen-bond networks. HBonanza, which can be used to analyze single structures or the many structures of a molecular dynamics trajectory, is open source and python implemented, making it easily editable, customizable, and platform independent. Unlike many other freely available hydrogen-bond analysis tools, HBonanza provides not only a text-based table describing the hydrogen-bond network, but also a Tcl script to facilitate visualization in VMD, a popular molecular visualization program. Visualization in other programs is also possible. A copy of HBonanza can be obtained free of charge from http://www.nbcr.net/hbonanza. PMID:21880522

High-pressure modulation of the structure of the bacterial photochemical reaction center at physiological and cryogenic temperatures

NASA Astrophysics Data System (ADS)

Timpmann, Kõu; Kangur, Liina; Lõhmus, Ants; Freiberg, Arvi

2017-07-01

The optical absorption and fluorescence response to external high pressure of the reaction center membrane chromoprotein complex from the wild-type non-sulfur photosynthetic bacterium Rhodobacter sphaeroides was investigated using the native pigment cofactors as local molecular probes of the reaction center structure at physiological (ambient) and cryogenic (79 K) temperatures. In detergent-purified complexes at ambient temperature, abrupt blue shift and accompanied broadening of the special pair band was observed at about 265 MPa. These reversible in pressure features were assigned to a pressure-induced rupture of a lone hydrogen bond that binds the photo-chemically active L-branch primary electron donor bacteriochlorophyll cofactor to the surrounding protein scaffold. In native membrane-protected complexes the hydrogen bond rupture appeared significantly restricted and occurred close to about 500 MPa. The free energy change associated with the rupture of the special pair hydrogen bond in isolate complexes was estimated to be equal to about 12 kJ mol-1. In frozen samples at cryogenic temperatures the hydrogen bond remained apparently intact up to the maximum utilized pressure of 600 MPa. In this case, however, heterogeneous spectral response of the cofactors from the L-and M-branches was observed due to anisotropic build-up of the protein structure. While in solid phase, the special pair fluorescence as a function of pressure exactly followed the respective absorption spectrum at a constant Stokes shift, at ambient temperature, the two paths began to deviate strongly from one other at the hydrogen bond rupture pressure. This effect was tentatively interpreted by different emission properties of hydrogen-bound and hydrogen-unbound special pair exciton states.

Enormous Hydrogen Bond Strength Enhancement through π-Conjugation Gain: Implications for Enzyme Catalysis.

PubMed

Wu, Chia-Hua; Ito, Keigo; Buytendyk, Allyson M; Bowen, K H; Wu, Judy I

2017-08-22

Surprisingly large resonance-assistance effects may explain how some enzymes form extremely short, strong hydrogen bonds to stabilize reactive oxyanion intermediates and facilitate catalysis. Computational models for several enzymic residue-substrate interactions reveal that when a π-conjugated, hydrogen bond donor (XH) forms a hydrogen bond to a charged substrate (Y - ), XH can become significantly more π-electron delocalized, and this "extra" stabilization may boost the [XH···Y - ] hydrogen bond strength by ≥15 kcal/mol. This reciprocal relationship departs from the widespread pK a concept (i.e., the idea that short, strong hydrogen bonds form when the interacting moieties have matching pK a values), which has been the rationale for enzymic acid-base reactions. The findings presented here provide new insight into how short, strong hydrogen bonds could form in enzymes.

The two faces of hydrogen-bond strength on triple AAA-DDD arrays.

PubMed

Lopez, Alfredo Henrique Duarte; Caramori, Giovanni Finoto; Coimbra, Daniel Fernando; Parreira, Renato Luis Tame; da Silva, Éder Henrique

2013-12-02

Systems that are connected through multiple hydrogen bonds are the cornerstone of molecular recognition processes in biology, and they are increasingly being employed in supramolecular chemistry, specifically in molecular self-assembly processes. For this reason, the effects of different substituents (NO2, CN, F, Cl, Br, OCH3 and NH2) on the electronic structure, and consequently on the magnitude of hydrogen bonds in triple AAA-DDD arrays (A=acceptor, D=donor) were evaluated in the light of topological [electron localization function (ELF) and quantum theory of atoms in molecules (QTAIM)], energetic [Su-Li energy-decomposition analysis (EDA) and natural bond orbital analysis (NBO)], and geometrical analysis. The results based on local H-bond descriptors (geometries, QTAIM, ELF, and NBO) indicate that substitutions with electron-withdrawing groups on the AAA module tend to strengthen, whereas electron-donating substituents tend to weaken the covalent character of the AAA-DDD intermolecular H-bonds, and also indicate that the magnitude of the effect is dependent on the position of substitution. In contrast, Su-Li EDA results show an opposite behavior when compared to local H-bond descriptors, indicating that electron-donating substituents tend to increase the magnitude of H-bonds in AAA-DDD arrays, and thus suggesting that the use of local H-bond descriptors describes the nature of H bonds only partially, not providing enough insight about the strength of such H bonds. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

2002-01-01

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.

Chemical Constraints Governing the Origin of Metabolism: The Thermodynamic Landscape of Carbon Group Transformations under Mild Aqueous Conditions

NASA Astrophysics Data System (ADS)

Weber, Arthur L.

2002-08-01

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (ΔG) were estimated for four types of reactions of biochemical importance - carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (ΔG < -3.5 kcal/mol), reversible (ΔG between +/-3.5 kcal/mol), or unfavorable (ΔG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.

Hydrogen anion and subgap states in amorphous In-Ga-Zn-O thin films for TFT applications

NASA Astrophysics Data System (ADS)

Bang, Joonho; Matsuishi, Satoru; Hosono, Hideo

2017-06-01

Hydrogen is an impurity species having an important role in the physical properties of semiconductors. Despite numerous studies, the role of hydrogen in oxide semiconductors remains an unsolved puzzle. This situation arises from insufficient information about the chemical state of the impurity hydrogen. Here, we report direct evidence for anionic hydrogens bonding to metal cations in amorphous In-Ga-Zn-O (a-IGZO) thin films for thin-film transistors (TFT) applications and discuss how the hydrogen impurities affect the electronic structure of a-IGZO. Infrared absorption spectra of self-standing a-IGZO thin films prepared by sputtering reveal the presence of hydrogen anions as a main hydrogen species (concentration is ˜1020 cm-3) along with the hydrogens in the form of the hydroxyl groups (˜1020 cm-3). Density functional theory calculations show that bonds between these hydride ions with metal centers give rise to subgap states above the top of the valence band, implying a crucial role of anionic hydrogen in the negative bias illumination stress instability commonly observed in a-IGZO TFTs.

Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

PubMed

Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

2016-05-05

Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes.

Short Carboxylic Acid–Carboxylate Hydrogen Bonds Can Have Fully Localized Protons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A.

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15–0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor–acceptor distance criteria for amore » LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O–O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O–O distance with increasing H-bond donor pK a. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid–carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.« less

Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.

PubMed

Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A

2017-01-17

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨d O-O ⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pK a . This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

Solid-state acid-base interactions in complexes of heterocyclic bases with dicarboxylic acids: crystallography, hydrogen bond analysis, and 15N NMR spectroscopy.

PubMed

Li, Z Jane; Abramov, Yuriy; Bordner, Jon; Leonard, Jason; Medek, Ales; Trask, Andrew V

2006-06-28

A cancer candidate, compound 1, is a weak base with two heterocyclic basic nitrogens and five hydrogen-bonding functional groups, and is sparingly soluble in water rendering it unsuitable for pharmaceutical development. The crystalline acid-base pairs of 1, collectively termed solid acid-base complexes, provide significant increases in the solubility and bioavailability compared to the free base, 1. Three dicarboxylic acid-base complexes, sesquisuccinate 2, dimalonate 3, and dimaleate 4, show the most favorable physicochemical profiles and are studied in greater detail. The structural analyses of the three complexes using crystal structure and solid-state NMR reveal that the proton-transfer behavior in these organic acid-base complexes vary successively correlating with Delta pKa. As a result, 2 is a neutral complex, 3 is a mixed ionic and zwitterionic complex and 4 is an ionic salt. The addition of the acidic components leads to maximized hydrogen bond interactions forming extended three-dimensional networks. Although structurally similar, the packing arrangements of the three complexes are considerably different due to the presence of multiple functional groups and the flexible backbone of 1. The findings in this study provide insight into the structural characteristics of complexes involving heterocyclic bases and carboxylic acids, and demonstrate that X-ray crystallography and 15N solid-state NMR are truly complementary in elucidating hydrogen bonding interactions and the degree of proton transfer of these complexes.

Electronic structure, hydrogen bonding and spectroscopic profile of a new 1,2,4-triazole-5(4H)-thione derivative: A combined experimental and theoretical (DFT) analysis

NASA Astrophysics Data System (ADS)

Al-Tamimi, Abdul-Malek S.

2016-09-01

Density functional theory has been implemented to study the electronic structure, molecular properties and vibrational spectra of 3-(adamantan-1-yl)-4-(4-chlorophenyl)-1H-1,2,4-triazole-5(4H)-thione, a novel 1,2,4-triazole-5(4H)-thione derivative. Hydrogen bonded dimer of the title molecule has been studied using B3LYP, M06-2X and X3LYP functionals at 6-311++ G(d,p) level of theory. The intermolecular hydrogen bonding has been studied using NBO analysis of the dimer. Bader's AIM theory was also used to evaluate the strength as well as the hydrogen bonding characteristics. Experimental FT-IR and FT-Raman spectra of the title molecule were related with the spectral data obtained with DFT/B3LYP method. The 1H NMR chemical shifts of the title molecule were calculated by the GIAO method and compared with experimental results. Dipole moment, polarizability (α), first order static hyperpolarizability (β) along with molecular electrostatic potential surface have been calculated. Frequency-dependent first hyperpolarizabilities, β(-2ω;ω,ω) and β(-ω;ω,0) have also been evaluated to study the non-linear optical behavior of the title compound. UV-Vis spectrum of the title molecule was recorded and TD-DFT method has been used to calculate six lowest excited states and the corresponding excitation energies.

On the nature of hydrogen bonding between the phosphatidylcholine head group and water and dimethylsulfoxide

NASA Astrophysics Data System (ADS)

Dabkowska, Aleksandra P.; Lawrence, M. Jayne; McLain, Sylvia E.; Lorenz, Christian D.

2013-01-01

Molecular dynamics simulations are used to provide a detailed investigation of the hydrogen bond networks around the phosphatidylcholine (PC) head group in 1,2-dipropionyl-sn-glycero-3-phosphocholine in pure water, 10 mol.% and 30 mol.% dimethylsulfoxide (DMSO)-water solutions. Specifically, it is observed that DMSO replaces those water molecules that are within the first solvation shell of the choline, phosphate and ester groups of the PC head group, but are not hydrogen-bonded to the group. The effect of the presence of DMSO on the hydrogen bond network around the PC head groups of the lipid changes with the concentration of DMSO. In comparison to the hydrogen bond network observed in the pure water system, the number of hydrogen-bonded chains of solvent molecules increases slightly for the 10 mol.% DMSO system, while, in the 30 mol.% DMSO system, the number of hydrogen-bonded chains of solvent molecules decreases.

The Different Sensitive Behaviors of a Hydrogen-Bond Acidic Polymer-Coated SAW Sensor for Chemical Warfare Agents and Their Simulants

PubMed Central

Long, Yin; Wang, Yang; Du, Xiaosong; Cheng, Luhua; Wu, Penglin; Jiang, Yadong

2015-01-01

A linear hydrogen-bond acidic (HBA) linear functionalized polymer (PLF), was deposited onto a bare surface acoustic wave (SAW) device to fabricate a chemical sensor. Real-time responses of the sensor to a series of compounds including sarin (GB), dimethyl methylphosphonate (DMMP), mustard gas (HD), chloroethyl ethyl sulphide (2-CEES), 1,5-dichloropentane (DCP) and some organic solvents were studied. The results show that the sensor is highly sensitive to GB and DMMP, and has low sensitivity to HD and DCP, as expected. However, the sensor possesses an unexpected high sensitivity toward 2-CEES. This good sensing performance can’t be solely or mainly attributed to the dipole-dipole interaction since the sensor is not sensitive to some high polarity solvents. We believe the lone pair electrons around the sulphur atom of 2-CEES provide an electron-rich site, which facilitates the formation of hydrogen bonding between PLF and 2-CEES. On the contrary, the electron cloud on the sulphur atom of the HD molecule is offset or depleted by its two neighbouring strong electron-withdrawing groups, hence, hydrogen bonding can hardly be formed. PMID:26225975

Crystalline Organic Pigment-Based Field-Effect Transistors.

PubMed

Zhang, Haichang; Deng, Ruonan; Wang, Jing; Li, Xiang; Chen, Yu-Ming; Liu, Kewei; Taubert, Clinton J; Cheng, Stephen Z D; Zhu, Yu

2017-07-05

Three conjugated pigment molecules with fused hydrogen bonds, 3,7-diphenylpyrrolo[2,3-f]indole-2,6(1H,5H)-dione (BDP), (E)-6,6'-dibromo-[3,3'-biindolinylidene]-2,2'-dione (IIDG), and 3,6-di(thiophen-2-yl)-2,5-dihydropyrrolo-[3,4-c]pyrrole-1,4-dione (TDPP), were studied in this work. The insoluble pigment molecules were functionalized with tert-butoxylcarbonyl (t-Boc) groups to form soluble pigment precursors (BDP-Boc, IIDG-Boc, and TDPP-Boc) with latent hydrogen bonding. The single crystals of soluble pigment precursors were obtained. Upon simple thermal annealing, the t-Boc groups were removed and the soluble pigment precursor molecules with latent hydrogen bonding were converted into the original pigment molecules with fused hydrogen bonding. Structural analysis indicated that the highly crystalline soluble precursors were directly converted into highly crystalline insoluble pigments, which are usually only achievable by gas-phase routes like physical vapor transport. The distinct crystal structure after the thermal annealing treatment suggests that fused hydrogen bonding is pivotal for the rearrangement of molecules to form a new crystal in solid state, which leads to over 2 orders of magnitude enhancement in charge mobility in organic field-effect transistor (OFET) devices. This work demonstrated that crystalline OFET devices with insoluble pigment molecules can be fabricated by their soluble precursors. The results indicated that a variety of commercially available conjugated pigments could be potential active materials for high-performance OFETs.

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

PubMed Central

Sigala, Paul A.; Fafarman, Aaron T.; Schwans, Jason P.; Fried, Stephen D.; Fenn, Timothy D.; Caaveiro, Jose M. M.; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A.; Boxer, Steven G.; Herschlag, Daniel

2013-01-01

Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol–Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations. PMID:23798390

Dye Aggregation and Complex Formation Effects in 7-(Diethylamino)-coumarin-3-carboxylic Acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xiaogang; Cole, Jacqueline M.; Chow, Philip C. Y.

2014-06-19

7-(Diethylamino)-coumarin-3-carboxylic acid (1) has been used as a laser dye, fluorescent label, and biomedical inhibitor in many different applications. Although this dye is typically used in the solution phase, it is prone to molecular aggregation, resulting in many inconsistent optoelectronic properties being reported in the literature. In this paper, the UV—vis absorption and fluorescence spectra of 1 are investigated in three representative solvents: cyclohexane [nonpolar and non-hydrogen bonding (NHB)], ethanol (moderately polar and hydrogen-bond accepting/donating), and DMSO (strongly polar and hydrogen-bond accepting). These experimental results, in conjunction with (time-dependent) density functional theory (DFT/TDDFT) based quantum calculations, have led to themore » identification of the J-aggregates of 1, and rationalized its different aggregation characteristic in cyclohexane in contrast to that of another similar compound, coumarin 343. We show here that these aggregates are largely responsible for the anomalous optoelectronic properties of this compound. In addition, DFT calculations and 1H NMR spectroscopy measurements suggest that the intramolecular hydrogen bond in 1 could be "opened up" in hydrogen-bond accepting solvents, affording significant molecular conformational changes and complex formation effects. The comprehensive understanding of the molecular aggregation and complex formation mechanisms of 1 acquired through this work forms a foundation for the knowledge-based molecular design of organic dyes with tailored aggregation tendencies or anti-aggregation characteristics to cater for different opapplications.« less

Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine.

PubMed

Müller, Andreas; Frey, Jann A; Leutwyler, Samuel

2005-06-16

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

Hydrogen bond dynamics in bulk alcohols.

PubMed

Shinokita, Keisuke; Cunha, Ana V; Jansen, Thomas L C; Pshenichnikov, Maxim S

2015-06-07

Hydrogen-bonded liquids play a significant role in numerous chemical and biological phenomena. In the past decade, impressive developments in multidimensional vibrational spectroscopy and combined molecular dynamics-quantum mechanical simulation have established many intriguing features of hydrogen bond dynamics in one of the fundamental solvents in nature, water. The next class of a hydrogen-bonded liquid--alcohols--has attracted much less attention. This is surprising given such important differences between water and alcohols as the imbalance between the number of hydrogen bonds, each molecule can accept (two) and donate (one) and the very presence of the hydrophobic group in alcohols. Here, we use polarization-resolved pump-probe and 2D infrared spectroscopy supported by extensive theoretical modeling to investigate hydrogen bond dynamics in methanol, ethanol, and isopropanol employing the OH stretching mode as a reporter. The sub-ps dynamics in alcohols are similar to those in water as they are determined by similar librational and hydrogen-bond stretch motions. However, lower density of hydrogen bond acceptors and donors in alcohols leads to the appearance of slow diffusion-controlled hydrogen bond exchange dynamics, which are essentially absent in water. We anticipate that the findings herein would have a potential impact on fundamental chemistry and biology as many processes in nature involve the interplay of hydrophobic and hydrophilic groups.

Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Semenov, M. A.; Blyzniuk, Iu. N.; Bolbukh, T. V.; Shestopalova, A. V.; Evstigneev, M. P.; Maleev, V. Ya.

2012-09-01

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (Cdbnd O and NH2) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

Facile fabrication of high-performance InGaZnO thin film transistor using hydrogen ion irradiation at room temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahn, Byung Du; Park, Jin-Seong; Chung, K. B., E-mail: kbchung@dongguk.edu

Device performance of InGaZnO (IGZO) thin film transistors (TFTs) are investigated as a function of hydrogen ion irradiation dose at room temperature. Field effect mobility is enhanced, and subthreshold gate swing is improved with the increase of hydrogen ion irradiation dose, and there is no thermal annealing. The electrical device performance is correlated with the electronic structure of IGZO films, such as chemical bonding states, features of the conduction band, and band edge states below the conduction band. The decrease of oxygen deficient bonding and the changes in electronic structure of the conduction band leads to the improvement of devicemore » performance in IGZO TFT with an increase of the hydrogen ion irradiation dose.« less

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

Stereospecific ring expansion from orthocyclophanes with central chirality to metacyclophanes with planar chirality.

PubMed

Ishida, Naoki; Sawano, Shota; Murakami, Masahiro

2014-01-01

Carbon-carbon bonds constitute the major framework of organic molecules and carbon-hydrogen bonds are abundant in their peripheries. Such nonpolar σ-bonds are thermodynamically stable and kinetically inert in general. Nonetheless, selective activation of those ubiquitous bonds may offer a straightforward method to construct and/or functionalize organic skeletons. Herein we describe ring expansion from orthocyclophanes to metacyclophanes occurring upon sequential action of light and a metal catalyst. Formally, specific non-strained carbon-hydrogen and carbon-carbon bonds are cleaved and exchanged without elimination of any leaving groups. Notably, the product is energetically uphill from the starting material, but the endergonic photocyclization step makes it possible to drive the transformation forward. The ring expansion is extended to the stereospecific synthesis of metacyclophanes possessing planar chirality, during which central chirality on a tertiary carbon is transferred to planar chirality.

Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

NASA Astrophysics Data System (ADS)

Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

2006-03-01

Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

Density functional theory study of the conformational space of an infinitely long polypeptide chain

NASA Astrophysics Data System (ADS)

Ireta, Joel; Scheffler, Matthias

2009-08-01

The backbone conformational space of infinitely long polyalanine is investigated with density-functional theory and mapping the potential energy surface in terms of (L, θ) cylindrical coordinates. A comparison of the obtained (L, θ) Ramachandran-like plot with results from an extended set of protein structures shows excellent conformity, with the exception of the polyproline II region. It is demonstrated the usefulness of infinitely long polypeptide models for investigating the influence of hydrogen bonding and its cooperative effect on the backbone conformations. The results imply that hydrogen bonding together with long-range electrostatics is the main actuator for most of the structures assumed by protein residues.

Theory after experiment on sensing mechanism of a newly developed sensor molecule: Converging or diverging?

NASA Astrophysics Data System (ADS)

Paul, Suvendu; Karar, Monaj; Das, Biswajit; Mallick, Arabinda; Majumdar, Tapas

2017-12-01

Fluoride ion sensing mechanism of 3,3‧-bis(indolyl)-4-chlorophenylmethane has been analyzed with density functional and time-dependent density functional theories. Extensive theoretical calculations on molecular geometry & energy, charge distribution, orbital energies & electronic distribution, minima on potential energy surface confirmed strong hydrogen bonded sensor-anion complex with incomplete proton transfer in S0. In S1, strong hydrogen bonding extended towards complete ESDPT. The distinct and single minima on the PES of the sensor-anion complex for both ground and first singlet excited states confirmed the concerted proton transfer mechanism. Present study well reproduced the experimental spectroscopic data and provided ESDPT as probable fluoride sensing mechanism.

Determining the Energetics of the Hydrogen Bond through FTIR: A Hands-On Physical Chemistry Lab Experiment

ERIC Educational Resources Information Center

Guerin, Abby C.; Riley, Kristi; Rupnik, Kresimir; Kuroda, Daniel G.

2016-01-01

Hydrogen bonds are very important chemical structures that are responsible for many unique and important properties of solvents, such as the solvation power of water. These distinctive features are directly related to the stabilization energy conferred by hydrogen bonds to the solvent. Thus, the characterization of hydrogen bond energetics has…

The tropolone-isobutylamine complex: a hydrogen-bonded troponoid without dominant π-π interactions.

PubMed

Vealey, Zachary N; Mercado, Brandon Q; Vaccaro, Patrick H

2016-10-01

Tropolone long has served as a model system for unraveling the ubiquitous phenomena of proton transfer and hydrogen bonding. This molecule, which juxtaposes ketonic, hydroxylic, and aromatic functionalities in a framework of minimal complexity, also has provided a versatile platform for investigating the synergism among competing intermolecular forces, including those generated by hydrogen bonding and aryl coupling. Small members of the troponoid family typically produce crystals that are stabilized strongly by pervasive π-π, C-H...π, or ion-π interactions. The organic salt (TrOH·iBA) formed by a facile proton-transfer reaction between tropolone (TrOH) and isobutylamine (iBA), namely isobutylammonium 7-oxocyclohepta-1,3,5-trien-1-olate, C 4 H 12 N + ·C 7 H 5 O 2 - , has been investigated by X-ray crystallography, with complementary quantum-chemical and statistical-database analyses serving to elucidate the nature of attendant intermolecular interactions and their synergistic effects upon lattice-packing phenomena. The crystal structure deduced from low-temperature diffraction measurements displays extensive hydrogen-bonding networks, yet shows little evidence of the aryl forces (viz. π-π, C-H...π, and ion-π interactions) that typically dominate this class of compounds. Density functional calculations performed with and without the imposition of periodic boundary conditions (the latter entailing isolated subunits) documented the specificity and directionality of noncovalent interactions occurring between the proton-donating and proton-accepting sites of TrOH and iBA, as well as the absence of aromatic coupling mediated by the seven-membered ring of TrOH. A statistical comparison of the structural parameters extracted for key hydrogen-bond linkages to those reported for 44 previously known crystals that support similar binding motifs revealed TrOH·iBA to possess the shortest donor-acceptor distances of any troponoid-based complex, combined with unambiguous signatures of enhanced proton-delocalization processes that putatively stabilize the corresponding crystalline lattice and facilitate its surprisingly rapid formation under ambient conditions.

Molecular dynamics simulation study of hydrogen bonding in aqueous poly(ethylene oxide) solutions.

PubMed

Smith, G D; Bedrov, D; Borodin, O

2000-12-25

A molecular dynamics simulation study of hydrogen bonding in poly(ethylene oxide) (PEO)/water solutions was performed. PEO-water and water-water hydrogen bonding manifested complex dependence on both composition and temperature. Strong water clustering in concentrated solutions was seen. Saturation of hydrogen bonding at w(p) approximately equal to 0.5 and a dramatic decrease in PEO-water hydrogen bonding with increasing temperature, consistent with experimentally observed closed-loop phase behavior, were observed. Little tendency toward intermolecular bridging of PEO chains by water molecules was seen.

The Born-Oppenheimer molecular simulations of infrared spectra of crystalline poly-(R)-3-hydroxybutyrate with analysis of weak Csbnd H⋯Odbnd C hydrogen bonds

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Wójcik, Marek J.; Sato, Harumi; Nakajima, Takahito; Ozaki, Yukihiro

2017-06-01

In this letter we present results of study of weak Csbnd H⋯Odbnd C hydrogen bonds of crystalline poly-(R)-3-hydroxybutyrate (PHB) by using Born-Oppenheimer molecular dynamics. The polymeric structure and IR spectra of PHB result from the presence of the weak hydrogen bonds. We applied the post-molecular dynamics analysis to consider a Cdbnd O motion as indirectly involved in the hydrogen bonds. Quantization of the nuclear motion of the oxygens was done to perform detailed analysis of the strength and properties of the Cdbnd O bands involved in the weak hydrogen bonds. We have also shown the dynamic character of the weak hydrogen bond interactions.

Theoretical study on the polar hydrogen-π (Hp-π) interactions between protein side chains

PubMed Central

2013-01-01

Background In the study of biomolecular structures and interactions the polar hydrogen-π bonds (Hp-π) are an extensive molecular interaction type. In proteins 11 of 20 natural amino acids and in DNA (or RNA) all four nucleic acids are involved in this type interaction. Results The Hp-π in proteins are studied using high level QM method CCSD/6-311 + G(d,p) + H-Bq (ghost hydrogen basis functions) in vacuum and in solutions (water, acetonitrile, and cyclohexane). Three quantum chemical methods (B3LYP, CCSD, and CCSD(T)) and three basis sets (6-311 + G(d,p), TZVP, and cc-pVTZ) are compared. The Hp-π donors include R2NH, RNH2, ROH, and C6H5OH; and the acceptors are aromatic amino acids, peptide bond unit, and small conjugate π-groups. The Hp-π interaction energies of four amino acid pairs (Ser-Phe, Lys-Phe, His-Phe, and Tyr-Phe) are quantitatively calculated. Conclusions Five conclusion points are abstracted from the calculation results. (1) The common DFT method B3LYP fails in describing the Hp-π interactions. On the other hand, CCSD/6-311 + G(d,p) plus ghost atom H-Bq can yield better results, very close to the state-of-the-art method CCSD(T)/cc-pVTZ. (2) The Hp-π interactions are point to π-plane interactions, possessing much more interaction conformations and broader energy range than other interaction types, such as common hydrogen bond and electrostatic interactions. (3) In proteins the Hp-π interaction energies are in the range 10 to 30 kJ/mol, comparable or even larger than common hydrogen bond interactions. (4) The bond length of Hp-π interactions are in the region from 2.30 to 3.00 Å at the perpendicular direction to the π-plane, much longer than the common hydrogen bonds (~1.9 Å). (5) Like common hydrogen bond interactions, the Hp-π interactions are less affected by solvation effects. PMID:23705926

The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations

NASA Astrophysics Data System (ADS)

Li, Yin; Lukács, András; Bordács, Sándor; Móczár, János; Nyitrai, Miklós; Hebling, János

2018-02-01

Low-frequency modes of L-Asp and L-Asn were studied in the range from 0.1 to 3.0 THz using time-domain Terahertz spectroscopy and density functional theory calculation. The results show that PBE-D2 shows more success than BLYP-D2 in prediction of THz absorption spectra. To compare their low-frequency modes, we adopted ;vibrational character ID strips; proposed by Schmuttenmaer and coworkers [Journal of Physical Chemistry B, 117, 10444(2013)]. We found that the most intense THz absorption peaks of two compounds both involve severe distortion of their hydrogen bonding networks. Due to less rigid hydrogen bonding network in L-Asp, the side chain (carboxyl group) of L-Asp exhibits larger motions than that (carboxamide group) of L-Asn in low-frequency modes.

Analytical model for three-dimensional Mercedes-Benz water molecules.

PubMed

Urbic, T

2012-06-01

We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature.

Analytical model for three-dimensional Mercedes-Benz water molecules

NASA Astrophysics Data System (ADS)

Urbic, T.

2012-06-01

We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature.

Pseudosymmetric fac-di-aqua-trichlorido[(di-methyl-phosphor-yl)methanaminium-κO]manganese(II).

PubMed

Reiss, Guido J

2013-05-01

In the title compound, [Mn(C3H11NOP)Cl3(H2O)2], the Mn(II) metal center has a distorted o-cta-hedral geometry, coordinated by the three chloride ligands showing a facial arrangement. Two water mol-ecules and the O-coordinated dpmaH cation [dpmaH = (di-methyl-phosphor-yl)methanaminium] complete the coordination sphere. Each complex mol-ecule is connected to its neighbours by O-H⋯Cl and N-H⋯Cl hydrogen bonds. Two of the chloride ligands and the two water ligands form a hydrogen-bonded polymeric sheet in the ab plane. Furthermore, these planes are connected to adjacent planes by hydrogen bonds from the aminium function of cationic dpmaH ligand. A pseudo-mirror plane perpendicular to the b axis in the chiral space group P21 is observed together with inversion twinning [ratio = 0.864 (5):0.136 (5)].

Analytical model for three-dimensional Mercedes-Benz water molecules

PubMed Central

Urbic, T.

2013-01-01

We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature. PMID:23005100

Methyl group dynamics in paracetamol and acetanilide: probing the static properties of intermolecular hydrogen bonds formed by peptide groups

NASA Astrophysics Data System (ADS)

Johnson, M. R.; Prager, M.; Grimm, H.; Neumann, M. A.; Kearley, G. J.; Wilson, C. C.

1999-06-01

Measurements of tunnelling and librational excitations for the methyl group in paracetamol and tunnelling excitations for the methyl group in acetanilide are reported. In both cases, results are compared with molecular mechanics calculations, based on the measured low temperature crystal structures, which follow an established recipe. Agreement between calculated and measured methyl group observables is not as good as expected and this is attributed to the presence of comprehensive hydrogen bond networks formed by the peptide groups. Good agreement is obtained with a periodic quantum chemistry calculation which uses density functional methods, these calculations confirming the validity of the one-dimensional rotational model used and the crystal structures. A correction to the Coulomb contribution to the rotational potential in the established recipe using semi-emipircal quantum chemistry methods, which accommodates the modified charge distribution due to the hydrogen bonds, is investigated.

Hydrogen Bond Induces Hierarchical Self-Assembly in Liquid-Crystalline Block Copolymers.

PubMed

Huang, Shuai; Pang, Linlin; Chen, Yuxuan; Zhou, Liming; Fang, Shaoming; Yu, Haifeng

2018-03-01

Microphase-separated structures of block copolymers (BCs) with a size of sub-10 nm are usually obtained by hydrogen-bond-induced self-assembly of BCs through doping with small molecules as functional additives. Here, fabrication of hierarchically self-assembled sub-10 nm structures upon microphase separation of amphiphilic liquid-crystalline BCs (LCBCs) at the existence of hydrogen bonds but without any dopants is reported. The newly introduced urethane groups in the side chain of the hydrophobic block of LCBCs interact with the ether groups of the hydrophilic poly(ethylene oxide) (PEO) block, leading to imperfect crystallization of the PEO blocks. Both crystalline and amorphous domains coexist in the separated PEO phase, enabling a lamellar structure to appear inside the PEO nanocylinders. This provides an elegant method to fabricate controllable sub-10 nm microstructures in well-defined polymer systems without the introduction of any dopants. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-02-22

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.

Hydrogen bonding. Part 18. The nature of the OHF hydrogen bond in choline fluoride

NASA Astrophysics Data System (ADS)

Harmon, Kenneth M.; Madeira, Susan L.; Jacks, Marshan J.; Avci, Günsel F.; Thiel, Anne C.

1985-05-01

The infrared spectrum of the OHF hydrogen bond in choline fluoride is completely different from the spectra of the electrostatic O—H⋯X hydrogen bonds in the other choline halides; however, this spectrum cannot be accounted for in terms of a "very strong" covalent OHF bond such as those found in carboxylic acid—fluoride ion complexes or postulated for betaine hydrofluoride. The spectrum of choline fluoride is interpreted best in terms of an intermediate type of unsymmetrical hydrogen bond ( r° O⋯F = ˜ 256 pm) which shows strong intensity enhancement for the first overtone of the OHF bending vibration.

Atomic Origins of the Self-Healing Function in Cement–Polymer Composites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Manh-Thuong; Wang, Zheming; Rod, Kenton A.

Motivated by recent advances in self-healing cement and epoxy polymer composites, we present a combined ab initio molecular dynamics and sum frequency generation (SFG) spectroscopy study of a calcium-silicate-hydrate/polymer interface. On stable, low-defect surfaces, the polymer only weakly adheres through coordination and hydrogen bonding interactions and can be easily mobilized towards defected surfaces. Conversely, on fractured surfaces, the polymer strongly anchors through ionic Ca-O bonds resulting from the deprotonation of polymer hydroxyl groups. In addition, polymer S-S groups are turned away from the cement/polymer interface, allowing for the self-healing function within the polymer. The overall elasticity and healing properties ofmore » these composites stem from a flexible hydrogen bonding network that can readily adapt to surface morphology. The theoretical vibrational signals associated with the proposed cement-polymer interfacial chemistry were confirmed experimentally by SFG spectroscopy.« less

Carbon–hydrogen (C–H) bond activation at PdIV: a Frontier in C–H functionalization catalysis

PubMed Central

Topczewski, Joseph J.

2015-01-01

The direct functionalization of carbon–hydrogen (C–H) bonds has emerged as a versatile strategy for the synthesis and derivatization of organic molecules. Among the methods for C–H bond activation, catalytic processes that utilize a PdII/PdIV redox cycle are increasingly common. The C–H activation step in most of these catalytic cycles is thought to occur at a PdII centre. However, a number of recent reports have suggested the feasibility of C–H cleavage occurring at PdIV complexes. Importantly, these latter processes often result in complementary reactivity and selectivity relative to analogous transformations at PdII. This mini review highlights proposed examples of C–H activation at PdIV centres. Applications of this transformation in catalysis as well as mechanistic details obtained from stoichiometric model studies are discussed. Furthermore, challenges and future perspectives for the field are reviewed. PMID:25544882

Carbon-Hydrogen (C-H) Bond Activation at PdIV: A Frontier in C-H Functionalization Catalysis.

PubMed

Topczewski, Joseph J; Sanford, Melanie S

2015-01-01

The direct functionalization of carbon-hydrogen (C-H) bonds has emerged as a versatile strategy for the synthesis and derivatization of organic molecules. Among the methods for C-H bond activation, catalytic processes that utilize a Pd II /Pd IV redox cycle are increasingly common. The C-H activation step in most of these catalytic cycles is thought to occur at a Pd II centre. However, a number of recent reports have suggested the feasibility of C-H cleavage occurring at Pd IV complexes. Importantly, these latter processes often result in complementary reactivity and selectivity relative to analogous transformations at Pd II . This Mini Review highlights proposed examples of C-H activation at Pd IV centres. Applications of this transformation in catalysis as well as mechanistic details obtained from stoichiometric model studies are discussed. Furthermore, challenges and future perspectives for the field are reviewed.

Atomic Origins of the Self-Healing Function in Cement-Polymer Composites.

PubMed

Nguyen, Manh-Thuong; Wang, Zheming; Rod, Kenton A; Childers, M Ian; Fernandez, Carlos; Koech, Phillip K; Bennett, Wendy D; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

2018-01-24

Motivated by recent advances in self-healing cement and epoxy polymer composites, we present a combined ab initio molecular dynamics and sum frequency generation (SFG) vibrational spectroscopy study of a calcium-silicate-hydrate/polymer interface. On stable, low-defect surfaces, the polymer only weakly adheres through coordination and hydrogen bonding interactions and can be easily mobilized toward defected surfaces. Conversely, on fractured surfaces, the polymer strongly anchors through ionic Ca-O bonds resulting from the deprotonation of polymer hydroxyl groups. In addition, polymer S-S groups are turned away from the cement-polymer interface, allowing for the self-healing function within the polymer. The overall elasticity and healing properties of these composites stem from a flexible hydrogen bonding network that can readily adapt to surface morphology. The theoretical vibrational signals associated with the proposed cement-polymer interfacial chemistry were confirmed experimentally by SFG vibrational spectroscopy.

Regioselective synthesis of C3 alkylated and arylated benzothiophenes

NASA Astrophysics Data System (ADS)

Shrives, Harry J.; Fernández-Salas, José A.; Hedtke, Christin; Pulis, Alexander P.; Procter, David J.

2017-03-01

Benzothiophenes are heterocyclic constituents of important molecules relevant to society, including those with the potential to meet modern medical challenges. The construction of molecules would be vastly more efficient if carbon-hydrogen bonds, found in all organic molecules, can be directly converted into carbon-carbon bonds. In the case of elaborating benzothiophenes, functionalization of carbon-hydrogen bonds at carbon-number 3 (C3) is markedly more demanding than at C2 due to issues of regioselectivity (C3 versus C2), and the requirement of high temperatures, precious metals and the installation of superfluous directing groups. Herein, we demonstrate that synthetically unexplored but readily accessible benzothiophene S-oxides serve as novel precursors for C3-functionalized benzothiophenes. Employing an interrupted Pummerer reaction to capture and then deliver phenol and silane coupling partners, we have discovered a directing group-free method that delivers C3-arylated and -alkylated benzothiophenes with complete regioselectivity, under metal-free and mild conditions.

A theoretical study of hydrogen complexes of the X sbnd H-π type between propyne and HF, HCL or HCN

NASA Astrophysics Data System (ADS)

Tavares, Alessandra M.; da Silva, Washington L. V.; Lopes, Kelson C.; Ventura, Elizete; Araújo, Regiane C. M. U.; do Monte, Silmar A.; da Silva, João Bosco P.; Ramos, Mozart N.

2006-05-01

The present manuscript reports a systematic investigation of the basis set dependence of some properties of hydrogen-bonded (π type) complexes formed by propyne and a HX molecule, where X = F, Cl and CN. The calculations have been performed at Hartree-Fock, MP2 and B3LYP levels. Geometries, H-bond energies and vibrational have been considered. The more pronounced effects on the structural parameters of the isolated molecules, as a result of complexation, are verified on RC tbnd C and HX bond lengths. As compared to double-ζ (6-31G **), triple-ζ (6-311G **) basis set leads to an increase of RC tbnd C bond distance, at all three computational levels. In the case where diffuse functions are added to both hydrogen and 'heavy' atoms, the effect is more pronounced. The propyne-HX structural parameters are quite similar to the corresponding parameters of acetylene-HX complexes, at all levels. The largest difference is obtained for hydrogen bond distance, RH, with a smaller value for propyne-HX complex, indicating a stronger bond. Concerning the electronic properties, the results yield the following ordering for H-bond energies, Δ E: propyne⋯HF > propyne⋯HCl > propyne⋯HCN. It is also important to point out that the inclusion of BSSE and zero-point energies (ZPE) corrections cause significant changes on Δ E. The smaller effect of ZPE is obtained for propyne⋯HCN at HF/6-311++G ** level, while the greatest difference is obtained at MP2/6-31G ** level for propyne⋯HF system. Concerning the IR vibrational it was obtained that larger shift can be associated with stronger hydrogen bonds. The more pronounced effect on the normal modes of the isolated molecule after the complexation is obtained for H sbnd X stretching frequency, which is shifted downward.

Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

NASA Astrophysics Data System (ADS)

Arjunan, V.; Thirunarayanan, S.; Marchewka, M. K.; Mohan, S.

2017-10-01

The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

Structural relaxation in the hydrogen-bonding liquids N-methylacetamide and water studied by optical Kerr effect spectroscopy.

PubMed

Turton, David A; Wynne, Klaas

2008-04-21

Structural relaxation in the peptide model N-methylacetamide (NMA) is studied experimentally by ultrafast optical Kerr effect spectroscopy over the normal-liquid temperature range and compared to the relaxation measured in water at room temperature. It is seen that in both hydrogen-bonding liquids, beta relaxation is present, and in each case, it is found that this can be described by the Cole-Cole function. For NMA in this temperature range, the alpha and beta relaxations are each found to have an Arrhenius temperature dependence with indistinguishable activation energies. It is known that the variations on the Debye function, including the Cole-Cole function, are unphysical, and we introduce two general modifications: One allows for the initial rise of the function, determined by the librational frequencies, and the second allows the function to be terminated in the alpha relaxation.

Active sites and states in the heterogeneous catalysis of carbon-hydrogen bonds.

PubMed

Somorjai, Gabor A; Marsh, Anderson L

2005-04-15

C-H bond activation for several alkenes (ethylene, propylene, isobutene, cyclohexene and 1-hexene) and alkanes (methane, ethane, n-hexane, 2-methylpentane and 3-methylpentane) has been studied on the (111) crystal face of platinum as a function of temperature at low (10(-6) Torr) and high (>/=1 Torr) pressures in the absence and presence of hydrogen pressures (>/=10 Torr). Sum frequency generation (SFG) vibrational spectroscopy has been used to characterize the adsorbate structures and high pressure scanning tunnelling microscopy (HP-STM) has been used to monitor their surface mobility under reaction conditions during hydrogenation, dehydrogenation and CO poisoning. C-H bond dissociation occurs at low temperatures, approximately 250 K, for all of these molecules, although only at high pressures for the weakly bound alkanes because of their low desorption temperatures. Bond dissociation is known to be surface structure sensitive and we find that it is also accompanied by the restructuring of the metal surface. The presence of hydrogen slows down dehydrogenation and for some of the molecules it influences the molecular rearrangement, thus altering reaction selectivity. Surface mobility of adsorbates is essential to produce catalytic activity. When surface diffusion is inhibited by CO adsorption, ordered surface structures form and the reaction is poisoned. Ethylene hydrogenation is surface structure insensitive, while cyclohexene hydrogenation and dehydrogenation are structure sensitive. n-Hexane and other C6 alkanes form either upright or flat-lying molecules on the platinum surface which react to produce branched isomers or benzene, respectively.

Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

PubMed

Takezawa, Yusuke; Shionoya, Mitsuhiko

2012-12-18

With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional DNA molecules such as artificial DNAzymes and DNA machines. In addition, the metallo-base pairing system is a powerful tool for the construction of homogeneous and heterogeneous metal arrays, which can lead to DNA-based nanomaterials such as electronic wires and magnetic devices. Recently researchers have investigated these systems as enzyme replacements, which may offer an additional contribution to chemical biology and synthetic biology through the expansion of the genetic alphabet.

A tensegrity model for hydrogen bond networks in proteins.

PubMed

Bywater, Robert P

2017-05-01

Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger - covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance ("closure") is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins ("domains") as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating elements in fibrous proteins.

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.

PubMed

Hayakawa, Daichi; Nishiyama, Yoshiharu; Mazeau, Karim; Ueda, Kazuyoshi

2017-09-08

Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A). Copyright © 2017 Elsevier Ltd. All rights reserved.

Sensitivity of hydrogen bonds of DNA and RNA to hydration, as gauged by 1JNH measurements in ethanol-water mixtures.

PubMed

Manalo, Marlon N; Kong, Xiangming; LiWang, Andy

2007-04-01

Hydrogen-bond lengths of nucleic acids are (1) longer in DNA than in RNA, and (2) sequence dependent. The physicochemical basis for these variations in hydrogen-bond lengths is unknown, however. Here, the notion that hydration plays a significant role in nucleic acid hydrogen-bond lengths is tested. Watson-Crick N1...N3 hydrogen-bond lengths of several DNA and RNA duplexes are gauged using imino 1J(NH) measurements, and ethanol is used as a cosolvent to lower water activity. We find that 1J(NH) values of DNA and RNA become less negative with added ethanol, which suggests that mild dehydration reduces hydrogen-bond lengths even as the overall thermal stabilities of these duplexes decrease. The 1J(NH) of DNA are increased in 8 mol% ethanol to those of RNA in water, which suggests that the greater hydration of DNA plays a significant role in its longer hydrogen bonds. The data also suggest that ethanol-induced dehydration is greater for the more hydrated G:C base pairs and thereby results in greater hydrogen-bond shortening than for the less hydrated A:T/U base pairs of DNA and RNA.

A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

NASA Astrophysics Data System (ADS)

Vijaya Pandiyan, B.; Kolandaivel, P.; Deepa, P.

2014-06-01

Hydrogen bonds and their strength were analysed based on their X-H proton-donor bond properties and the parameters of the H-Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

Disilane chemisorption on Si(x)Ge(1-x)(100)-(2 x 1): molecular mechanisms and implications for film growth rates.

PubMed

Ng, Rachel Qiao-Ming; Tok, E S; Kang, H Chuan

2009-07-28

At low temperatures, hydrogen desorption is known to be the rate-limiting process in silicon germanium film growth via chemical vapor deposition. Since surface germanium lowers the hydrogen desorption barrier, Si(x)Ge((1-x)) film growth rate increases with the surface germanium fraction. At high temperatures, however, the molecular mechanisms determining the epitaxial growth rate are not well established despite much experimental work. We investigate these mechanisms in the context of disilane adsorption because disilane is an important precursor used in film growth. In particular, we want to understand the molecular steps that lead, in the high temperature regime, to a decrease in growth rate as the surface germanium increases. In addition, there is a need to consider the issue of whether disilane adsorbs via silicon-silicon bond dissociation or via silicon-hydrogen bond dissociation. It is usually assumed that disilane adsorption occurs via silicon-silicon bond dissociation, but in recent work we provided theoretical evidence that silicon-hydrogen bond dissociation is more important. In order to address these issues, we calculate the chemisorption barriers for disilane on silicon germanium using first-principles density functional theory methods. We use the calculated barriers to estimate film growth rates that are then critically compared to the experimental data. This enables us to establish a connection between the dependence of the film growth rate on the surface germanium content and the kinetics of the initial adsorption step. We show that the generally accepted mechanism where disilane chemisorbs via silicon-silicon bond dissociation is not consistent with the data for film growth kinetics. Silicon-hydrogen bond dissociation paths have to be included in order to give good agreement with the experimental data for high temperature film growth rate.

Supramolecular network through Nsbnd H…O, Osbnd H…O and Csbnd H…O hydrogen bonding interaction and density functional theory studies of 4-methylanilinium-3-carboxy-4-hydroxybenzenesulphonate crystal

NASA Astrophysics Data System (ADS)

Rajkumar, M.; Muthuraja, P.; Dhandapani, M.; Chandramohan, A.

2018-02-01

By utilizing the hydrogen bonding strategy, 4-methylanilinium-3-hydroxy-4-corboxy-benzenesulphonate (4MABS), an organic proton transfer molecular salt was synthesized and single crystals of it were successfully grown by slow solvent evaporation solution growth technique at ambient temperature. The 1H and 13C NMR spectra were recorded to establish the molecular structure of the title salt. The single crystal XRD analysis reveals that the title salt crystallizes in monoclinic crystal system with centrosymmetric space group, P21/n. Further, the title salt involves extensive intermolecular Nsbnd H…O, Osbnd H…O and Csbnd H…O as well as intramolecular Osbnd H…O hydrogen bonding interactions to construct supramolecular architecture. All quantum chemical calculations were performed at the level of density functional theory (DFT) with B3LYP functional using 6-311G (d,p) basis atomic set. The photoluminescence spectrum was recorded to explore the emission property of the title crystal. The presence of the various vibrational modes and functional groups in the synthesized salt was confirmed by FT-IR studies. The thermal behaviour of title crystal was established employing TG/DTA analyses. The mechanical properties of the grown crystal were determined by Vicker's microhardness studies. Dielectric measurements were carried out on the grown crystal at a different temperature to evaluate electrical properties.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

PubMed

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Hydrogen bonds and heat diffusion in α-helices: a computational study.

PubMed

Miño, German; Barriga, Raul; Gutierrez, Gonzalo

2014-08-28

Recent evidence has shown a correlation between the heat diffusion pathways and the known allosteric communication pathways in proteins. Allosteric communication in proteins is a central, yet unsolved, problem in biochemistry, and the study and characterization of the structural determinants that mediate energy transfer among different parts of proteins is of major importance. In this work, we characterized the role of hydrogen bonds in diffusivity of thermal energy for two sets of α-helices with different abilities to form hydrogen bonds. These hydrogen bonds can be a constitutive part of the α-helices or can arise from the lateral chains. In our in vacuo simulations, it was observed that α-helices with a higher possibility of forming hydrogen bonds also had higher rates of thermalization. Our simulations also revealed that heat readily flowed through atoms involved in hydrogen bonds. As a general conclusion, according to our simulations, hydrogen bonds fulfilled an important role in heat diffusion in structural patters of proteins.

Tunneling readout of hydrogen-bonding based recognition

PubMed Central

Chang, Shuai; He, Jin; Kibel, Ashley; Lee, Myeong; Sankey, Otto; Zhang, Peiming; Lindsay, Stuart

2009-01-01

Hydrogen bonding has a ubiquitous role in electron transport1,2 and in molecular recognition, with DNA base-pairing being the best known example.3 Scanning tunneling microscope (STM) images4 and measurements of the decay of tunnel-current as a molecular junction is pulled apart by the STM tip, 5 are sensitive to hydrogen-bonded interactions. Here we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA basepairs. Junctions that are held together by three hydrogen bonds per basepair (e.g., guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per basepair (e.g., adenine-thymine interactions). Similar, but less-pronounced, effects are observed on the approach of the tunneling probe, implying that hydrogen-bond dependent attractive forces also have a role in determining the rise of current. These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal. PMID:19421214

Selective Nitrate Recognition by a Halogen-Bonding Four-Station [3]Rotaxane Molecular Shuttle.

PubMed

Barendt, Timothy A; Docker, Andrew; Marques, Igor; Félix, Vítor; Beer, Paul D

2016-09-05

The synthesis of the first halogen bonding [3]rotaxane host system containing a bis-iodo triazolium-bis-naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo-triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion-rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the (1) H NMR anion binding results. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Molecular reorganization of selected quinoline derivatives in the ground and excited states—Investigations via static DFT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Błaziak, Kacper; Panek, Jarosław J.; Jezierska, Aneta, E-mail: aneta.jezierska@chem.uni.wroc.pl

2015-07-21

Quinoline derivatives are interesting objects to study internal reorganizations due to the observed excited-state-induced intramolecular proton transfer (ESIPT). Here, we report on computations for selected 12 quinoline derivatives possessing three kinds of intramolecular hydrogen bonds. Density functional theory was employed for the current investigations. The metric and electronic structure simulations were performed for the ground state and first excited singlet and triplet states. The computed potential energy profiles do not show a spontaneous proton transfer in the ground state, whereas excited states exhibit this phenomenon. Atoms in Molecules (AIM) theory was applied to study the nature of hydrogen bonding, whereasmore » Harmonic Oscillator Model of aromaticity index (HOMA) provided data of aromaticity evolution as a derivative of the bridge proton position. The AIM-based topological analysis confirmed the presence of the intramolecular hydrogen bonding. In addition, using the theory, we were able to provide a quantitative illustration of bonding transformation: from covalent to the hydrogen. On the basis of HOMA analysis, we showed that the aromaticity of both rings is dependent on the location of the bridge proton. Further, the computed results were compared with experimental data available. Finally, ESIPT occurrence was compared for the three investigated kinds of hydrogen bridges, and competition between two bridges in one molecule was studied.« less

An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase

NASA Astrophysics Data System (ADS)

Golden, Emily; Yu, Li-Juan; Meilleur, Flora; Blakeley, Matthew P.; Duff, Anthony P.; Karton, Amir; Vrielink, Alice

2017-01-01

The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2014-06-01

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

Computational study of the process of hydrogen bond breaking: the case of the formamide-formic acid complex.

PubMed

Pacios, Luis F

2006-11-15

MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) quantum calculations are used to study the formamide-formic acid complex (FFAC), a system bound by two hydrogen bonds, N--H...O and O--H...O, that forms a bond ring at equilibrium. When the intermolecular separation between monomers R increases, this ring opens at a distance for which the weaker N--H...O bond breaks remaining the stronger O--H...O bond. The computational study characterizes that process addressing changes of interaction energy DeltaE, structure and properties of the electron density rho(r) as well as spatial distributions of rho(r), the electrostatic potential U(r), and the electron localization function eta(r). It is shown that the spatial derivatives of DeltaE, the topology of rho(r), and qualitative changes noticed in U(r) = 0 isocontours allow to identify a precise distance R for which one can say the N--H...O hydrogen bond has broken. Both levels of theory predict essentially the same changes of structure and electron properties associated to the process of breaking and virtually identical distances at which it takes place. (c) 2006 Wiley Periodicals, Inc. J Comput Chem, 2006.

Formation of molecular complexes of salicylic acid, acetylsalicylic acid, and methyl salicylate in a mixture of supercritical carbon dioxide with a polar cosolvent

NASA Astrophysics Data System (ADS)

Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.

2015-08-01

The solvate structures formed by salicylic acid, acetylsalicylic acid, and methyl salicylate in supercritical (SC) carbon dioxide with a polar cosolvent (methanol, 0.03 mole fractions) at a density of 0.7 g/cm3 and a temperature of 318 K were studied by the molecular dynamics method. Salicylic and acetylsalicylic acids were found to form highly stable hydrogen-bonded complexes with methanol via the hydrogen atom of the carboxyl group. For methyl salicylate in which the carboxyl hydrogen is substituted by a methyl radical, the formation of stable hydrogen bonds with methanol was not revealed. The contribution of other functional groups of the solute to the interactions with the cosolvent was much smaller. An analysis of correlations between the obtained data and the literature data on the cosolvent effect on the solubility of the compounds in SC CO2 showed that the dissolving ability of SC CO2 with respect to a polar organic substance in the presence of a cosolvent increased only when stable hydrogen-bonded complexes are formed between this substance and the cosolvent.

Peroxotantalate-Based Ionic Liquid Catalyzed Epoxidation of Allylic Alcohols with Hydrogen Peroxide.

PubMed

Ma, Wenbao; Chen, Chen; Kong, Kang; Dong, Qifeng; Li, Kun; Yuan, Mingming; Li, Difan; Hou, Zhenshan

2017-05-29

The efficient and environmentally benign epoxidation of allylic alcohols has been attained by using new kinds of monomeric peroxotantalate anion-functionalized ionic liquids (ILs=[P 4,4,4,n ] 3 [Ta(O) 3 (η-O 2 )], P 4,4,4,n =quaternary phosphonium cation, n=4, 8, and 14), which have been developed and their structures determined accordingly. This work revealed the parent anions of the ILs underwent structural transformation in the presence of H 2 O 2 . The formed active species exhibited excellent catalytic activity, with a turnover frequency for [P 4,4,4,4 ] 3 [Ta(O) 3 (η-O 2 )] of up to 285 h -1 , and satisfactory recyclability in the epoxidation of various allylic alcohols under very mild conditions by using only one equivalent of hydrogen peroxide as an oxidant. NMR studies showed the reaction was facilitated through a hydrogen-bonding mechanism, in which the peroxo group (O-O) of the peroxotantalate anion served as the hydrogen-bond acceptor and hydroxyl group in the allylic alcohols served as the hydrogen-bond donor. This work demonstrates that simple monomeric peroxotantalates can catalyze epoxidation of allylic alcohols efficiently. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

First-principles study of hydrogen-bonded molecular conductor κ -H3(Cat-EDT-TTF/ST)2

NASA Astrophysics Data System (ADS)

Tsumuraya, Takao; Seo, Hitoshi; Kato, Reizo; Miyazaki, Tsuyoshi

2015-07-01

We theoretically study hydrogen-bonded molecular conductors synthesized recently, κ -H3(Cat-EDT-TTF) 2 and its diselena analog, κ -H3(Cat-EDT-ST) 2, by first-principles density functional theory calculations. In these crystals, two H(Cat-EDT-TTF/ST) units share a hydrogen atom with a short O-H-O hydrogen bond. The calculated band structure near the Fermi level shows a quasi-two-dimensional character with a rather large interlayer dispersion due to the absence of insulating layers, in contrast with conventional molecular conductors. We discuss effective low-energy models based on H(Cat-EDT-TTF/ST) units and its dimers, respectively, where the microscopic character of the orbitals composing them are analyzed. Furthermore, we find a stable structure which is different from the experimentally determined structure, where the shared hydrogen atom becomes localized to one of the oxygen atoms, in which charge disproportionation between the two types of H(Cat-EDT-TTF) units is associated. The calculated potential energy surface for the H atom is very shallow near the minimum points; therefore the probability of the H atom can be delocalized between the two O atoms.

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

PubMed

Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

2014-02-01

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.

PubMed

Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

2012-09-01

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment. Copyright © 2012 Elsevier B.V. All rights reserved.

Structural elucidation of antihemorrhage drug molecule Diethylammonium 2,5-dihydroxybenzene sulfonate - an insilico approach

NASA Astrophysics Data System (ADS)

Kumar, S. Anil; Bhaskar, BL

2018-02-01

Ab-initio computational study of antihemorrhage drug molecule diethylammonium 2,5-dihydroxybenzene sulfonate, popularly known as ethamsylate, has been attempted using Gaussian 09. The optimized molecular geometry has been envisaged using density functional theory method at B3LYP/6-311 basis set. Different geometrical parameters like bond lengths and bond angles were computed and compared against the experimental results available in literature. Fourier transform infrared scanning of the title molecule was performed and vibrational frequencies were also computed using Gaussian software. The presence of O-H---O hydrogen bonds between C6H5O5S- anions and N-H---O hydrogen bonds between anion and cation is evident in the computational studies also. In general, satisfactory agreement of concordance has been observed between computational and experimental results.

Experimental and Computational Exploration of para-Selective Silylation with a Hydrogen-Bonded Template.

PubMed

Maji, Arun; Guin, Srimanta; Feng, Sheng; Dahiya, Amit; Singh, Vikas Kumar; Liu, Peng; Maiti, Debabrata

2017-11-20

The regioselective conversion of C-H bonds into C-Si bonds is extremely important owing to the natural abundance and non-toxicity of silicon. Classical silylation reactions often suffer from poor functional group compatibility, low atom economy, and insufficient regioselectivity. Herein, we disclose a template-assisted method for the regioselective para silylation of toluene derivatives. A new template was designed, and the origin of selectivity was analyzed experimentally and computationally. An interesting substrate-solvent hydrogen-bonding interaction was observed. Kinetic, spectroscopic, and computational studies shed light on the reaction mechanism. The synthetic significance of this strategy was highlighted by the generation of a precursor of a potential lipophilic bioisostere of γ-aminobutyric acid (GABA), various late-stage diversifications, and by mimicking enzymatic transformations. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polymer films

DOEpatents

Granick, Steve; Sukhishvili, Svetlana A.

2004-05-25

A film contains a first polymer having a plurality of hydrogen bond donating moieties, and a second polymer having a plurality of hydrogen bond accepting moieties. The second polymer is hydrogen bonded to the first polymer.

Polymer films

DOEpatents

Granick, Steve [Champaign, IL; Sukhishvili, Svetlana A [Maplewood, NJ

2008-12-30

A film contains a first polymer having a plurality of hydrogen bond donating moieties, and a second polymer having a plurality of hydrogen bond accepting moieties. The second polymer is hydrogen bonded to the first polymer.

In situ study at high pressure and temperature of the environment of water in hydrous Na and Ca aluminosilicate melts and coexisting aqueous fluids

NASA Astrophysics Data System (ADS)

Le Losq, Charles; Dalou, Célia; Mysen, Bjorn O.

2017-07-01

The bonding and speciation of water dissolved in Na silicate and Na and Ca aluminosilicate melts were inferred from in situ Raman spectroscopy of the samples, in hydrothermal diamond anvil cells, while at crustal temperature and pressure conditions. Raman data were also acquired on Na silicate and Na and Ca aluminosilicate glasses, quenched from hydrous melts equilibrated at high temperature and pressure in a piston cylinder apparatus. In the hydrous melts, temperature strongly influences O-H stretching ν(O-H) signals, reflecting its control on the bonding of protons between different molecular complexes. Pressure and melt composition effects are much smaller and difficult to discriminate with the present data. However, the chemical composition of the melt + fluid system influences the differences between the ν(O-H) signals from the melts and the fluids and, hence, between their hydrogen partition functions. Quenching modifies the O-H stretching signals: strong hydrogen bonds form in the glasses below the glass transition temperature Tg, and this phenomenon depends on glass composition. Therefore, glasses do not necessarily record the O-H stretching signal shape in melts near Tg. The melt hydrogen partition function thus cannot be assessed with certainty using O-H stretching vibration data from glasses. From the present results, the ratio of the hydrogen partition functions of hydrous silicate melts and aqueous fluids mostly depends on temperature and the bulk melt + fluid system chemical composition. This implies that the fractionation of hydrogen isotopes between magmas and aqueous fluids in water-saturated magmatic systems with differences in temperature and bulk chemical composition will be different.

Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories.

PubMed

Chikalov, Igor; Yao, Peggy; Moshkov, Mikhail; Latombe, Jean-Claude

2011-02-15

Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration Δ. We model dependence of the output variable on the predictors by a regression tree. Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings. We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone.

Spectroscopically determined force field for water dimer: physically enhanced treatment of hydrogen bonding in molecular mechanics energy functions.

PubMed

Mannfors, Berit; Palmo, Kim; Krimm, Samuel

2008-12-11

Our ab initio transformed spectroscopically determined force field (SDFF) methodology emphasizes, in addition to accurate structure and energy performance, comparable prediction of vibrational properties in order to improve reproduction of interaction forces. It is now applied to the determination of a molecular mechanics (MM) force field for the water monomer and dimer as an initial step in developing a more physically based treatment of the hydrogen bonding that not only underlies condensed-phase water but also must be important in molecular-level protein-water interactions. Essential electrical components of the SDFF for monomer water are found to be the following: an off-plane charge distribution, this distribution consisting of four off-atom charge sites in traditional lone pair (LP) but also in inverted lone pair (ILP) positions; allowance for a diffuse size to these off-atom sites; and the incorporation of charge fluxes (i.e., the change in charge with change in internal coordinate). Parametrization of such an LP/ILP model together with the SDFF analytically transformed valence force field results in essentially exact agreement with ab initio (in this case MP2/6-31++G(d,p)) structure, electrical, and vibrational properties. Although we demonstrate that the properties of this monomer electrical model together with its van der Waals and polarization interactions are transferable to the dimer, this is not sufficient in reproducing comparable dimer properties, most notably the huge increase in infrared intensity of a donor OH stretch mode. This deficiency, which can be eliminated by a large dipole-derivative-determined change in the effective charge flux of the donor hydrogen-bonded OH bond, is not accounted for by the charge flux change in this bond due to the induction effects of the acceptor electric field alone, and can only be fully removed by an added bond flux associated with the extent of overlap of the wave functions of the two molecules. We show that this overlap charge flux (OCF) emulates an actual O-H...LP-O intermolecular dipole flux, reflecting the unitary nature of the hydrogen-bonded system in the context of MM-separable molecules. The effectiveness of incorporating the OCF noncanonical character demonstrates that a distinctively QM-unique property can be substantively represented in MM energy functions.

Allosteric Breakage of the Hydrogen Bond within the Dual-Histidine Motif in the Active Site of Human Pin1 PPIase.

PubMed

Wang, Jing; Tochio, Naoya; Kawasaki, Ryosuke; Tamari, Yu; Xu, Ning; Uewaki, Jun-Ichi; Utsunomiya-Tate, Naoko; Tate, Shin-Ichi

2015-08-25

Intimate cooperativity among active site residues in enzymes is a key factor for regulating elaborate reactions that would otherwise not occur readily. Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is the phosphorylation-dependent cis-trans peptidyl-prolyl isomerase (PPIase) that specifically targets phosphorylated Ser/Thr-Pro motifs. Residues C113, H59, H157, and T152 form a hydrogen bond network in the active site, as in the noted connection. Theoretical studies have shown that protonation to thiolate C113 leads to rearrangement of this hydrogen bond network, with switching of the tautomeric states of adjacent histidines (H59 and H157) [Barman, A., and Hamelberg, D. (2014) Biochemistry 53, 3839-3850]. This is called the "dual-histidine motif". Here, C113A and C113S Pin1 mutants were found to alter the protonation states of H59 according to the respective residue type replaced at C113, and the mutations resulted in disruption of the hydrogen bond within the dual-histidine motif. In the C113A mutant, H59 was observed to be in exchange between ε- and δ-tautomers, which widened the entrance of the active site cavity, as seen by an increase in the distance between residues A113 and S154. The C113S mutant caused H59 to exchange between the ε-tautomer and imidazolium while not changing the active site structure. Moreover, the imidazole ring orientations of H59 and H157 were changed in the C113S mutant. These results demonstrated that a mutation at C113 modulates the hydrogen bond network dynamics. Thus, C113 acts as a pivot to drive the concerted function among the residues in the hydrogen bond network, as theoretically predicted.

Molecular mechanism of gelation upon the addition of water to a solution of poly(acrylonitrile) in dimethylsulfoxide

NASA Astrophysics Data System (ADS)

Vettegren, V. I.; Kulik, V. B.; Savitskii, A. V.; Fetisov, O. I.; Usov, V. V.

2010-05-01

The solidification of a solution of poly(acrylonitrile) (PAN) in dimethylsulfoxide (DMSO) upon introduction of water into the solution is studied by Raman spectroscopy. In the absence of water, DMSO molecules are found to produce dipole-dipole bonds with PAN molecules. Upon the introduction of water, DMSO molecules produce hydrogen bonds with it and bands at 1005 and 1015 cm-1 appear in the Raman spectrum, which are assigned to the valence vibrations of S=O bonds involved in the hydrogen bonds. Simultaneously, water molecules produce hydrogen bonds with PAN molecules: R-C≡N...H-O-H...N≡C-R, where R is the carbon skeleton of a PAN molecule. Accordingly, a band at 2250 cm-1 arises in the Raman spectrum, which is assigned to the valence vibrations of C≡N bonds producing hydrogen bonds with a water molecule. When the water content is low and the DMSO concentration is high, the length of the hydrogen bonds varies in wide limits and the band at 2250 cm-1 is wide. As the water content rises, DMSO molecules come out of PAN, the variation of the hydrogen bond length in it decreases (the band at 2250 cm-1 narrows), and a high-viscosity system (gel) arises that consists of PAN molecules bonded to water molecules via “equally strong” hydrogen bonds.

Nonequilibrium 2-Hydroxyoctadecanoic Acid Monolayers: Effect of Electrolytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lendrum, Conrad D.; Ingham, Bridget; Lin, Binhua

2012-02-06

2-Hydroxyacids display complex monolayer phase behavior due to the additional hydrogen bonding afforded by the presence of the second hydroxy group. The placement of this group at the position {alpha} to the carboxylic acid functionality also introduces the possibility of chelation, a utility important in crystallization including biomineralization. Biomineralization, like many biological processes, is inherently a nonequilibrium process. The nonequilibrium monolayer phase behavior of 2-hydroxyoctadecanoic acid was investigated on each of pure water, calcium chloride, sodium bicarbonate and calcium carbonate crystallizing subphases as a precursor study to a model calcium carbonate biomineralizing system, each at a pH of {approx}6. Themore » role of the bicarbonate co-ion in manipulating the monolayer structure was determined by comparison with monolayer phase behavior on a sodium chloride subphase. Monolayer phase behavior was probed using surface pressure/area isotherms, surface potential, Brewster angle microscopy, and synchrotron-based grazing incidence X-ray diffraction and X-ray reflectivity. Complex phase behavior was observed for all but the sodium chloride subphase with hydrogen bonding, electrostatic and steric effects defining the symmetry of the monolayer. On a pure water subphase hydrogen bonding dominates with three phases coexisting at low pressures. Introduction of calcium ions into the aqueous subphase ensures strong cation binding to the surfactant head groups through chelation. The monolayer becomes very unstable in the presence of bicarbonate ions within the subphase due to short-range hydrogen bonding interactions between the monolayer and bicarbonate ions facilitated by the sodium cation enhancing surfactant solubility. The combined effects of electrostatics and hydrogen bonding are observed on the calcium carbonate crystallizing subphase.« less

Controlling Internal Organization of Multilayer Poly(methacrylic acid) Hydrogels with Polymer Molecular Weight

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozlovskaya, Veronika; Zavgorodnya, Oleksandra; Ankner, John F.

Here, we report on tailoring the internal architecture of multilayer-derived poly(methacrylic acid) (PMAA) hydrogels by controlling the molecular weight of poly(N-vinylpyrrolidone) (PVPON) in hydrogen-bonded (PMAA/PVPON) layer-by-layer precursor films. The hydrogels are produced by cross-linking PMAA in the spin-assisted multilayers followed by PVPON release. We found that the thickness, morphology, and architecture of hydrogen-bonded films and the corresponding hydrogels are significantly affected by PVPON chain length. For all systems, an increase in PVPON molecular weight from M w = 2.5 to 1300 kDa resulted in increased total film thickness. We also show that increasing polymer M w smooths the hydrogen-bonded filmmore » surfaces but roughens those of the hydrogels. Using deuterated dPMAA marker layers in neutron reflectometry measurements, we found that hydrogen-bonded films reveal a high degree of stratification which is preserved in the cross-linked films. We observed dPMAA to be distributed more widely in the hydrogen-bonded films prepared with small M w PVPON due to the greater mobility of short-chain PVPON. Furthermore, these variations in the distribution of PMAA are erased after cross-linking, resulting in a distribution of dPMAA over about two bilayers for all M w but being somewhat more widely distributed in the films templated with higher M w PVPON. Finally, our results yield new insights into controlling the organization of nanostructured polymer networks using polymer molecular weight and open opportunities for fabrication of thin films with well-organized architecture and controllable function.« less

Controlling Internal Organization of Multilayer Poly(methacrylic acid) Hydrogels with Polymer Molecular Weight

DOE PAGES

Kozlovskaya, Veronika; Zavgorodnya, Oleksandra; Ankner, John F.; ...

2015-11-16

Here, we report on tailoring the internal architecture of multilayer-derived poly(methacrylic acid) (PMAA) hydrogels by controlling the molecular weight of poly(N-vinylpyrrolidone) (PVPON) in hydrogen-bonded (PMAA/PVPON) layer-by-layer precursor films. The hydrogels are produced by cross-linking PMAA in the spin-assisted multilayers followed by PVPON release. We found that the thickness, morphology, and architecture of hydrogen-bonded films and the corresponding hydrogels are significantly affected by PVPON chain length. For all systems, an increase in PVPON molecular weight from M w = 2.5 to 1300 kDa resulted in increased total film thickness. We also show that increasing polymer M w smooths the hydrogen-bonded filmmore » surfaces but roughens those of the hydrogels. Using deuterated dPMAA marker layers in neutron reflectometry measurements, we found that hydrogen-bonded films reveal a high degree of stratification which is preserved in the cross-linked films. We observed dPMAA to be distributed more widely in the hydrogen-bonded films prepared with small M w PVPON due to the greater mobility of short-chain PVPON. Furthermore, these variations in the distribution of PMAA are erased after cross-linking, resulting in a distribution of dPMAA over about two bilayers for all M w but being somewhat more widely distributed in the films templated with higher M w PVPON. Finally, our results yield new insights into controlling the organization of nanostructured polymer networks using polymer molecular weight and open opportunities for fabrication of thin films with well-organized architecture and controllable function.« less

Supramolecular hydrogen-bonding network in 1-(diaminomethylene)thiouron-1-ium 4-hydroxybenzenesulfonate crystal

NASA Astrophysics Data System (ADS)

Perpétuo, Genivaldo J.; Gonçalves, Rafael S.; Janczak, Jan

2015-09-01

The single crystals of 1-(diaminomethylene)thiouron-1-ium 4-hydroxybenzenesulfonate were grown using a solution growth technique. The compound crystallises in the centrosymmetric P21/c space group of the monoclinic system. The conformation of the 1-(diaminomethylene)thiouron-1-ium cation is not strictly planar, but twisted. Both arms of the cation are oppositely rotated by 8.5(1)° around the Csbnd N bonds involving the central N atom. The arrangement of oppositely charged components, i.e. 1-(diaminomethylene)thiouron-1-ium cations and 4-hydroxybenzenesulfonate anions in the crystal is mainly determined by ionic and hydrogen-bonding interactions forming supramolecular network. The possible hydrogen-bonding interactions between cation and anion units were analysed on the basis of molecular orbital calculations. The obtained deuterated analogue crystallises similar as H-compound in the monoclinic system (P21/c) with quite similar lattice parameters. The compound was also characterised by the FT-IR and Raman spectroscopies. The characteristic bands of the functional and skeletal groups of the protiated and deuterated analogue of 1-(diaminomethylene)thiouron-1-ium 4-hydroxybenzenesulfonate are discussed.

The dynamics of solvation dictates the conformation of polyethylene oxide in aqueous, isobutyric acid and binary solutions.

PubMed

Dahal, Udaya R; Dormidontova, Elena E

2017-04-12

Polymers hydrogen-bonding with solvent represent an important broad class of polymers, properties of which depend on solvation. Using atomistic molecular dynamics simulations with the OPLS/AA force field we investigate the effect of hydrogen bonding on PEO conformation and chain mobility by comparing its behavior in isobutyric acid and aqueous solutions. In agreement with experimental data, we found that in isobutyric acid PEO forms a rather rigid extended helical structure, while in water it assumes a highly flexible coil conformation. We show that the difference in PEO conformation and flexibility is the result of the hydrogen bond stability and overall solvent dynamics near PEO. Isobutyric acid forms up to one hydrogen bond per repeat unit of PEO and interacts with PEO for a prolonged period of time, thereby stabilizing the helical structure of the polymer and reducing its segmental mobility. In contrast, water forms on average 1.2 hydrogen bonds per repeat unit of PEO (with 60% of water forming a single hydrogen bond and 40% of water forming two hydrogen bonds) and resides near PEO for a noticeably shorter time than isobutyric acid, leading to the well-documented high segmental mobility of PEO in water. We also analyze PEO conformation, hydrogen bonding and segmental mobility in binary water/isobutyric acid solutions and find that in the phase separated region PEO resides in the isobutyric-rich phase forming about 25% of its hydrogen bonds with isobutyric acid and 75% with water. We show that the dynamics of solvation affects the equilibrium properties of macromolecules, such as conformation, and by mixing of hydrogen bond-donating solvents one can significantly alter both polymer conformation and its local dynamics.

Ab initio EPR parameters for dangling-bond defect complexes in silicon: Effect of Jahn-Teller distortion

NASA Astrophysics Data System (ADS)

Pfanner, Gernot; Freysoldt, Christoph; Neugebauer, Jörg; Gerstmann, Uwe

2012-05-01

A dangling bond (db) is an important point defect in silicon. It is realized in crystalline silicon by defect complexes of the monovacancy V with impurities. In this work, we present spin-polarized density-functional theory calculations of EPR parameters (g and hyperfine tensors) within the GIPAW formalism for two kinds of db defect complexes. The first class characterizes chemically saturated db systems, where three of the four dangling bonds of the isolated vacancy are saturated by hydrogen (VH3) or hydrogen and oxygen (hydrogen-oxygen complex, VOH). The second kind of db consists of systems with a Jahn-Teller distortion, where the vacancy includes either a substitutional phosphorus atom (the E center, VP) or a single hydrogen atom (VH). For all systems we obtain excellent agreement with available experimental data, and we are therefore able to quantify the effect of the Jahn-Teller distortion on the EPR parameters. Furthermore we study the influence of strain to obtain further insights into the structural and electronic characteristics of the considered defects.

Activation of carbon-hydrogen bonds and dihydrogen by 1,2-CH-addition across metal-heteroatom bonds.

PubMed

Webb, Joanna R; Burgess, Samantha A; Cundari, Thomas R; Gunnoe, T Brent

2013-12-28

The controlled conversion of hydrocarbons to functionalized products requires selective C-H bond cleavage. This perspective provides an overview of 1,2-CH-addition of hydrocarbons across d(0) transition metal imido complexes and compares and contrasts these to examples of analogous reactions that involve later transition metal amide, hydroxide and alkoxide complexes with d(6) and d(8) metals.

Predictions of glass transition temperature for hydrogen bonding biomaterials.

PubMed

van der Sman, R G M

2013-12-19

We show that the glass transition of a multitude of mixtures containing hydrogen bonding materials correlates strongly with the effective number of hydroxyl groups per molecule, which are available for intermolecular hydrogen bonding. This correlation is in compliance with the topological constraint theory, wherein the intermolecular hydrogen bonds constrain the mobility of the hydrogen bonded network. The finding that the glass transition relates to hydrogen bonding rather than free volume agrees with our recent finding that there is little difference in free volume among carbohydrates and polysaccharides. For binary and ternary mixtures of sugars, polyols, or biopolymers with water, our correlation states that the glass transition temperature is linear with the inverse of the number of effective hydroxyl groups per molecule. Only for dry biopolymer/sugar or sugar/polyol mixtures do we find deviations due to nonideal mixing, imposed by microheterogeneity.

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

PubMed

Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

2015-03-01

The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding. © 2014 Wiley Periodicals, Inc.

Removal of a hazardous heavy metal from aqueous solution using functionalized graphene and boron nitride nanosheets: Insights from simulations.

PubMed

Azamat, Jafar; Sattary, Batoul Shirforush; Khataee, Alireza; Joo, Sang Woo

2015-09-01

A computer simulation was performed to investigate the removal of Zn(2+) as a heavy metal from aqueous solution using the functionalized pore of a graphene nanosheet and boron nitride nanosheet (BNNS). The simulated systems were comprised of a graphene nanosheet or BNNS with a functionalized pore containing an aqueous ionic solution of zinc chloride. In order to remove heavy metal from an aqueous solution using the functionalized pore of a graphene nanosheet and BNNS, an external voltage was applied along the z-axis of the simulated box. For the selective removal of zinc ions, the pores of graphene and BNNS were functionalized by passivating each atom at the pore edge with appropriate atoms. For complete analysis systems, we calculated the potential of the mean force of ions, the radial distribution function of ion-water, the residence time of ions, the hydrogen bond, and the autocorrelation function of the hydrogen bond. Copyright © 2015 Elsevier Inc. All rights reserved.

The carbene insertion methodology for the catalytic functionalization of unreactive hydrocarbons: no classical C-H activation, but efficient C-H functionalization.

PubMed

Díaz-Requejo, M Mar; Belderrain, Tomás R; Nicasio, M Carmen; Pérez, Pedro J

2006-12-21

This contribution intends to highlight the use of the metal-catalyzed functionalization of unreactive carbon-hydrogen bonds by the carbene insertion methodology, that employs diazo compounds as the carbene source.

Tracking Co(I) Intermediate in operando in Photocatalytic Hydrogen Evolution by X-ray transient Absorption Spectroscopy and DFT Calculation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhi-Jun; Zhan, Fei; Xiao, Hongyan

X-ray transient absorption spectroscopy (XTA) and optical transient spectroscopy (OTA) were used to probe the Co(I) intermediate generated in situ from an aqueous photocatalytic hydrogen evolution system, with [RuII(bpy)3]Cl2·6H2O as the photosensitizer, ascorbic acid/ascorbate as the electron donor, and the Co-polypyridyl complex ([CoII(DPABpy) Cl]Cl) as the pre-catalyst. Upon exposure to light, the XTA measured at Co K-edge visualizes the grow and decay of the Co(I) intermediate, and reveals its Co-N bond contraction of 0.09 ± 0.03 Å. Density functional theory (DFT) calculations support the bond contraction and illustrate that the metal-to-ligand π back-bonding greatly stabilizes the penta-coordinated Co(I) intermediate, whichmore » provides easy photon access. To the best of our knowledge, this is the first example of capturing the penta-coordinated Co(I) intermediate in operando with bond contraction by XTA, thereby providing new insights for fundamental understanding of structure– function relationship of cobalt-based molecular catalysts.« less

The nature of hydrogen-bonding interactions in nonsteroidal anti-inflammatory drugs revealed by polarized IR spectroscopy

NASA Astrophysics Data System (ADS)

Hachuła, Barbara

2018-01-01

The influence of hydrogen-bonding interactions in the solid phase on the IR spectroscopic pattern of the νOsbnd H band of nonsteroidal anti-inflammatory drugs (NSAIDs) was studied experimentally by IR spectroscopy with the use of polarized light at two temperatures (293 K and 77 K) and in isotopic dilution. The neat and deuterated crystals of (S)-naproxen ((S)-NPX), (R)-flurbiprofen ((R)-FBP), (RS)-flurbiprofen ((RS)-FBP) and (RS)-ketoprofen ((RS)-KTP) were obtained by melt crystallization between the two squeezed CaF2 plates. The vibrational spectra of selected α-aryl propionic acid derivatives (2APAs) reflected the characteristics of their hydrogen-bond networks, i.e., 2APAs were characterized by the chain ((S)-NPX, (R)-FBP) and by dimeric ((RS)-FBP, (RS)-KTP) arrangement of hydrogen bonds in the crystal lattice. Spectroscopic results showed that the interchain (through-space) exciton coupling, between two laterally-spaced hydrogen bonds, dominates in the crystals of four NSAIDs. The same exciton coupled hydrogen bonds were also responsible for the H/D isotopic recognition mechanism in the crystalline spectra of deuterated 2APAs. The presented spectral results may help to predict the hydrogen bond motifs in the crystalline NSAIDs, which structures are not yet known, based on their IR spectra of hydrogen bond in the crystals.

Cooperatively enhanced ionic hydrogen bonds in Cl-(CH3OH)(1-3)Ar clusters.

PubMed

Beck, Jordan P; Lisy, James M

2010-09-23

Infrared predissociation (IRPD) spectra of Cl−(CH3OH)1-3Ar and Cl-(CH3OD)1-3Ar were obtained in the OH and CH stretching regions. The use of methanol-d1 was necessary to distinguish between CH stretches and hydrogen-bonded OH features. The spectra of Cl-(CH3OH)2-3Ar show intense features at frequencies lower than the CH stretches, indicating structures with very strong hydrogen bonds. These strong hydrogen bonds arise from structures in which a Cl-···methanol ionic hydrogen bond is cooperatively enhanced by the presence of a second shell and, in the case of Cl-(CH3OH)3Ar, a third shell methanol. The strongest hydrogen bond is observed in the Cl-(CH3OH)3Ar spectrum at 2733 cm-1, shifted a remarkable -948 cm-1 from the neutral, gas-phase methanol value. Harmonic, ab initio frequency calculations are not adequate in describing these strong hydrogen bonds. Therefore, we describe a simple computational approach to better approximate the hydrogen bond frequencies. Overall, the results of this study indicate that high-energy isomers are very efficiently trapped using our experimental method of introducing Cl- into neutral, cold methanol-argon clusters.

A Relativity Enhanced, Medium-Strong Au(I)···H-N Hydrogen Bond in a Protonated Phenylpyridine-Gold(I) Thiolate.

PubMed

Berger, Raphael J F; Schoiber, Jürgen; Monkowius, Uwe

2017-01-17

Gold is an electron-rich metal with a high electronegativity comparable to that of sulfur. Hence, hydrogen bonds of the Au(I)···H-E (E = electronegative element) type should be possible, but their existence is still under debate. Experimental results are scarce and often contradictory. As guidance for possible preparative work, we have theoretically investigated (ppyH)Au(SPh) (ppy = 2-phenylpyridine) bearing two monoanionic ligands which are not strongly electronegative at the same time to further increase the charge density on the gold(I) atom. The protonated pyridine nitrogen atom in ppy is geometrically ideally suited to place a proton in close proximity to the gold atom in a favorable geometry for a classical hydrogen bond arrangement. Indeed, the results of the calculations indicate that the hydrogen bonded conformation of (ppyH)Au(SPh) represents a minimum geometry with bond metrics in the expected range for medium-strong hydrogen bonds [r(N-H) = 1.043 Å, r(H···Au) = 2.060 Å, a(N-H···Au) = 141.4°]. The energy difference between the conformer containing the H···Au bond and another conformer without a hydrogen bond amounts to 7.8 kcal mol -1 , which might serve as an estimate of the hydrogen bond strength. Spectroscopic properties were calculated, yielding further characteristics of such hydrogen bonded gold species.

Genetic selection reveals the role of a buried, conserved polar residue

PubMed Central

Johnson, R. Jeremy; Lin, Shawn R.; Raines, Ronald T.

2007-01-01

The burial of nonpolar surface area is known to enhance markedly the conformational stability of proteins. The contribution from the burial of polar surface area is less clear. Here, we report on the tolerance to substitution of Ser75 of bovine pancreatic ribonuclease (RNase A), a residue that has the unusual attributes of being buried, conserved, and polar. To identify variants that retain biological function, we used a genetic selection based on the intrinsic cytotoxicity of ribonucleolytic activity. Cell growth at 30°C, 37°C, and 44°C correlated with residue size, indicating that the primary attribute of Ser75 is its small size. The side-chain hydroxyl group of Ser75 forms a hydrogen bond with a main-chain nitrogen. The conformational stability of the S75A variant, which lacks this hydrogen bond, was diminished by ΔΔG = 2.5 kcal/mol. Threonine, which can reinstate this hydrogen bond, provided a catalytically active RNase A variant at higher temperatures than did some smaller residues (including aspartate), indicating that a secondary attribute of Ser75 is the ability of its uncharged side chain to accept a hydrogen bond. These results provide insight on the imperatives for the conservation of a buried polar residue. PMID:17656580

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Yinshan; Zhu, Men; Laventure, Audrey

Surface grating decay measurements have been performed on three closely related molecular glasses to study the effect of intermolecular hydrogen bonds on surface diffusion. The three molecules are derivatives of bis(3,5-dimethyl-phenylamino)-1,3,5-triazine and differ only in the functional group R at the 2-position, with R being C 2H 5, OCH 3, and NHCH 3, and referred to as “Et”, “OMe”, and “NHMe”, respectively. Of the three molecules, NHMe forms more extensive intermolecular hydrogen bonds than Et and OMe and was found to have slower surface diffusion. For Et and OMe, surface diffusion is so fast that it replaces viscous flow asmore » the mechanism of surface grating decay as temperature is lowered. In contrast, no such transition was observed for NHMe under the same conditions, indicating significantly slower surface diffusion. This result is consistent with the previous finding that extensive intermolecular hydrogen bonds slow down surface diffusion in molecular glasses and is attributed to the persistence of hydrogen bonds even in the surface environment. Here, this result is also consistent with the lower stability of the vapor-deposited glass of NHMe relative to those of Et and OMe and supports the view that surface mobility controls the stability of vapor-deposited glasses.« less

The hydrogen-bond collective dynamics in liquid methanol

DOE PAGES

Bellissima, Stefano; Cunsolo, Alessandro; DePanfilis, Simone; ...

2016-12-20

The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HBmore » dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.« less

Structure and vibrational analysis of methyl 3-amino-2-butenoate.

PubMed

Berenji, Ali Reza; Tayyari, Sayyed Faramarz; Rahimizadeh, Mohammad; Eshghi, Hossein; Vakili, Mohammad; Shiri, Ali

2013-02-01

The molecular structure and vibrational spectra of methyl 3-(amino)-2-butenoate (MAB) and its deuterated analogous, D(3)MAB, were investigated using density functional theory (DFT) calculations. The geometrical parameters and harmonic vibrational wavenumbers of MAB and D(3)MAB were obtained at the B3LYP/6-311++G(d,p) level. The calculated vibrational wavenumbers were compared with the corresponding experimental results. The assignment of the IR and Raman spectra of MAB and D(3)MAB was facilitated by calculating the anharmonic wavenumbers at the B3LYP/6-311G(d,p) level as well as recording and calculating the MAB spectra in CCl(4) solution. The assigned normal modes were compared with a similar molecule, 4-amino-3-penten-2-one (APO). The theoretical results were in good agreement with the experimental data. All theoretical and experimental results indicate that substitution of a methyl group with a methoxy group considerably weakens the intramolecular hydrogen bond and reduces the π-electron delocalization in the chelated ring system. The IR spectra also indicate that in the solid state, MAB is not only engaged in an intramolecular hydrogen bond, but also forms an intermolecular hydrogen bond. However, the intermolecular hydrogen bond will be removed in dilute CCl(4) solution. Copyright © 2012 Elsevier B.V. All rights reserved.

The NiCl2-Li-arene(cat.) combination: a versatile reducing mixture.

PubMed

Alonso, Francisco; Yus, Miguel

2004-06-20

The NiCl2.2H2O-Li-arene(cat.) combination described in this tutorial review has shown to be a useful and versatile mixture able to reduce a broad range of functionalities bearing carbon-carbon multiple bonds, as well as carbon-heteroatom and heteroatom-heteroatom single and multiple bonds. The analogous deuterated combination, NiCl2.2D2O-Li-arene(cat.), allows the easy incorporation of deuterium in the reaction products. Alternatively, the anhydrous NiCl2-Li-arene (or polymer-supported arene)(cat.) system generates a highly reactive metallic nickel, which in the presence of molecular hydrogen at atmospheric pressure is able to catalyze the hydrogenation of almost the same type of functionalities mentioned above.

Theoretical study of hydrogen bonding interaction in nitroxyl (HNO) dimer: interrelationship of the two N-H...O blue-shifting hydrogen bonds.

PubMed

Liu, Ying; Liu, Wenqing; Li, Haiyang; Liu, Jianguo; Yang, Yong

2006-10-19

The hydrogen bonding interactions of the HNO dimer have been investigated using ab initio molecular orbital and density functional theory (DFT) with the 6-311++G(2d,2p) basis set. The natural bond orbital (NBO) analysis and atom in molecules (AIM) theory were applied to understand the nature of the interactions. The interrelationship between one N-H...O hydrogen bond and the other N-H...O hydrogen bond has been established by performing partial optimizations. The dimer is stabilized by the N-H...O hydrogen bonding interactions, which lead to the contractions of N-H bonds as well as the characteristic blue-shifts of the stretching vibrational frequencies nu(N-H). The NBO analysis shows that both rehybridization and electron density redistribution contribute to the large blue-shifts of the N-H stretching frequencies. A quantitative correlations of the intermolecular distance H...O (r(H...O)) with the parameters: rho at bond critical points (BCPs), s-characters of N atoms in N-H bonds, electron densities in the sigma*(N-H), the blue-shift degrees of nu(N-H) are presented. The relationship between the difference of rho (|Deltarho|) for the one hydrogen bond compared with the other one and the difference of interaction energy (DeltaE) are also illustrated. It indicates that for r(H...O) ranging from 2.05 to 2.3528 A, with increasing r(H...O), there is the descending tendency for one rho(H...O) and the ascending tendency for the other rho(H...O). r(H...O) ranging from 2.3528 to 2.85 A, there are descending tendencies for the two rho(H...O) with increasing r(H...O). On the potential energy surface of the dimer, the smaller the difference between one rho(H...O) and the other rho(H...O) is, the more stable the structure is. As r(H...O) increases, the blue-shift degrees of nu(N-H) decrease. The cooperative descending tendencies in s-characters of two N atoms with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H). Ranging from 2.05 to 2.55 A, the increase of the electron density in one sigma*(N-H) with elongating r(H...O) weakens the blue-shift degrees of nu(N-H), simultaneously, the decrease of the electron density in the other sigma*(N-H) with elongating r(H...O) strengthens the blue-shift degrees of nu(N-H). Ranging from 2.55 to 2.85 A, the cooperative ascending tendencies of the electron densities in two sigma*(N-H) with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H).

Hydrogen bonding pattern in N-benzoyl(- DL-)- L-phenylalanines as revealed by solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Potrzebowski, M. J.; Schneider, C.; Tekely, P.

1999-11-01

The nature of the hydrogen bonding pattern has been investigated in N-benzoyl- DL-phenylalanine ( 1) and N-benzoyl- L-phenylalanine ( 2) polymorphes by solid-state NMR spectroscopy. It has been shown that the multiple resonances of carboxyl carbon in 2 are directly connected to different types of hydrogen bonding. The differences in intermolecular distances of carboxyl groups involved in different types of hydrogen bonding have been visualized by the 2D exchange and 1D ODESSA experiments. Potential applications of such a new approach include the exploration of intermolecular distances in hydrogen bonded compounds with singly labeled biomolecules.

Density functional theory study on the ionization potentials and electron affinities of thymine-formamide complexes

NASA Astrophysics Data System (ADS)

Sun, Haitao; Tang, Ke; Li, Yanmin; Su, Chunfang; Zhou, Zhengyu; Wang, Zhizhong

The effect of hydrogen bond interactions on ionization potentials (IPs) and electron affinities (EAs) of thymine-formamide complexes (T-F) have been investigated employing the density functional theory B3LYP at 6-311++G(d, p) basis set level. All complexes experience a geometrical change on either electron detachment or attachment, and the change might be facilitated or hindered according to the strength of the hydrogen-bonding interaction involved. The strength of hydrogen bonds presents an opposite changing trend on the two processes. A more important role that H-bonding interaction plays in the process of electron attachment than in the process of electron detachment can be seen by a comparison of the IPs and EAs of complexes with that of isolated thymine. Futhermore, the EAs of isolated thymine are in good agreement with the experimental values (AEA is 0.79 eV, VEA is -0.29 eV [Wetmore et al., Chem Phys Lett 2000, 322, 129]). The calculated total NPA charge distributions reveal that nearly all the negative charges locate on thymine monomer in the anions and even in the cationic states, there are a few negative charges on thymine monomer. An analysis of dissociation energies predicts the processes T-F+→ T++ F and T-F- → T- + F to be the most energetically favorable for T-F+ and T-F-, respectively. Content:text/plain; charset="UTF-8"

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

PubMed Central

Nagy, Peter I.

2014-01-01

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

Theoretical Insights into Methane C–H Bond Activation on Alkaline Metal Oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aljama, Hassan; Nørskov, Jens K.; Abild-Pedersen, Frank

Here, we investigate the role of alkaline metal oxides (AMO) (MgO, CaO, and SrO) in activating the C–H bond in methane. We also use Density Functional Theory (DFT) and microkinetic modeling to study the catalytic elementary steps in breaking the C–H bond in methane and creating the methyl radical, a precursor prior to creating C2 products. We also study the effects of surface geometry on the catalytic activity of AMO by examining terrace and step sites. We observe that the process of activating methane depends strongly on the structure of the AMO. When the AMO surface is doped with anmore » alkali metal, the transition state (TS) structure has a methyl radical-like behavior, where the methyl radical interacts weakly with the AMO surface. In this case, the TS energy scales with the hydrogen binding energy. On pure AMO, the TS interacts with AMO surface oxygen as well as the metal atom on the surface, and consequently the TS energy scales with the binding energy of hydrogen and methyl. We study the activity of AMO using a mean-field microkinetic model. The results indicate that terrace sites have similar catalytic activity, with the exception of MgO(100). Step sites bind hydrogen more strongly, making them more active, and this confirms previously reported experimental results. We map the catalytic activity of AMO using a volcano plot with two descriptors: the methyl and the hydrogen binding energies, with the latter being a more significant descriptor. The microkinetic model results suggest that C–H bond dissociation is not always the rate-limiting step. At weak hydrogen binding, the reaction is limited by C–H bond activation. At strong hydrogen binding, the reaction is limited due to poisoning of the active site. We found an increase in activity of AMO as the basicity increased. Finally, the developed microkinetic model allows screening for improved catalysts using simple calculations of the hydrogen binding energy.« less

Theoretical Insights into Methane C–H Bond Activation on Alkaline Metal Oxides

DOE PAGES

Aljama, Hassan; Nørskov, Jens K.; Abild-Pedersen, Frank

2017-07-17

Here, we investigate the role of alkaline metal oxides (AMO) (MgO, CaO, and SrO) in activating the C–H bond in methane. We also use Density Functional Theory (DFT) and microkinetic modeling to study the catalytic elementary steps in breaking the C–H bond in methane and creating the methyl radical, a precursor prior to creating C2 products. We also study the effects of surface geometry on the catalytic activity of AMO by examining terrace and step sites. We observe that the process of activating methane depends strongly on the structure of the AMO. When the AMO surface is doped with anmore » alkali metal, the transition state (TS) structure has a methyl radical-like behavior, where the methyl radical interacts weakly with the AMO surface. In this case, the TS energy scales with the hydrogen binding energy. On pure AMO, the TS interacts with AMO surface oxygen as well as the metal atom on the surface, and consequently the TS energy scales with the binding energy of hydrogen and methyl. We study the activity of AMO using a mean-field microkinetic model. The results indicate that terrace sites have similar catalytic activity, with the exception of MgO(100). Step sites bind hydrogen more strongly, making them more active, and this confirms previously reported experimental results. We map the catalytic activity of AMO using a volcano plot with two descriptors: the methyl and the hydrogen binding energies, with the latter being a more significant descriptor. The microkinetic model results suggest that C–H bond dissociation is not always the rate-limiting step. At weak hydrogen binding, the reaction is limited by C–H bond activation. At strong hydrogen binding, the reaction is limited due to poisoning of the active site. We found an increase in activity of AMO as the basicity increased. Finally, the developed microkinetic model allows screening for improved catalysts using simple calculations of the hydrogen binding energy.« less

Palladium-Catalyzed Allylic C-H Bond Functionalization of Olefins

NASA Astrophysics Data System (ADS)

Liu, Guosheng; Wu, Yichen

Transition metal-mediated carbon-hydrogen bond cleavage and functionalization is a mechanistically interesting and synthetically attractive process. One of the important cases is the removal of a allylic hydrogen from an olefin by a PdII salt to yield a π-allylpalladium complex, followed by nucleophilic attack to efficient produce allylic derivatives. In contrast to the well-known allylic acetoxylation of cyclohexene, the reaction of open-chain olefins is fairly poor until recent several years. Some palladium catalytic systems have been reported to achieve allylic C-H functionalization, including acetoxylation, amination and alkylation of terminal alkenes. In the most of cases, ligand is crucial to the success of the transformation. This review surveys the recent development of palladium-catalyzed allylic C-H functionalziation of alkenes. These results promise a significant increase in the scope of olefin transformation.

Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: a comparison between density functional theory and density functional tight binding results.

PubMed

grosse Holthaus, Svea; Köppen, Susan; Frauenheim, Thomas; Ciacchi, Lucio Colombi

2014-06-21

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101̄0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.

Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: A comparison between density functional theory and density functional tight binding results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holthaus, Svea große; Köppen, Susan, E-mail: koeppen@hmi.uni-bremen.de; Frauenheim, Thomas

2014-06-21

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101{sup ¯}0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to formmore » predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.« less

Functionality of Immunoglobulin G and Immunoglobulin M Antibody Physisorbed on Cellulosic Films

PubMed Central

Huang, Ziwei; Raghuwanshi, Vikram Singh; Garnier, Gil

2017-01-01

The functionality and aging mechanism of antibodies physisorbed onto cellulosic films was investigated. Blood grouping antibodies immunoglobulin G (IgG) and immunoglobulin M (IgM) were adsorbed onto smooth cellulose acetate (CAF) and regenerated cellulose (RCF) films. Cellulose films and adsorbed IgG layers were characterized at the air and liquid interface by X-ray and neutron reflectivity (NR), respectively. Cellulose film 208 Å thick (in air) swell to 386 Å once equilibrated in water. IgG adsorbs from solution onto cellulose as a partial layer 62 Å thick. IgG and IgM antibodies were adsorbed onto cellulose and cellulose acetate films, air dried, and aged at room temperature for periods up to 20 days. Antibody functionality and surface hydrophobicity were measured everyday with the size of red blood cell (RBC) agglutinates (using RBC specific to IgG/IgM) and the water droplet contact angle, respectively. The functionality of the aged IgG/IgM decreases faster if physisorbed on cellulose than on cellulose acetate and correlates to surface hydrophobicity. IgG physisorbed on RCF or CAF age better and remain functional longer than physisorbed IgM. We found a correlation between antibody stability and hydrogen bond formation ability of the system, evaluated from antibody carbonyl concentration and cellulosic surface hydroxyl concentration. Antibody physisorbs on cellulose by weak dipole forces and hydrogen bonds. Strong hydrogen bonding contributes to the physisorption of antibody on cellulose into a non-functional configuration in which the molecule relaxes by rotation of hydophobic groups toward the air interface. PMID:28770196

Enantioselective C(sp3)‒H bond activation by chiral transition metal catalysts.

PubMed

Saint-Denis, Tyler G; Zhu, Ru-Yi; Chen, Gang; Wu, Qing-Feng; Yu, Jin-Quan

2018-02-16

Organic molecules are rich in carbon-hydrogen bonds; consequently, the transformation of C-H bonds to new functionalities (such as C-C, C-N, and C-O bonds) has garnered much attention by the synthetic chemistry community. The utility of C-H activation in organic synthesis, however, cannot be fully realized until chemists achieve stereocontrol in the modification of C-H bonds. This Review highlights recent efforts to enantioselectively functionalize C(sp 3 )-H bonds via transition metal catalysis, with an emphasis on key principles for both the development of chiral ligand scaffolds that can accelerate metalation of C(sp 3 )-H bonds and stereomodels for asymmetric metalation of prochiral C-H bonds by these catalysts. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Constraints on Biogenic Emplacement of Crystalline Calcium Carbonate and Dolomite

NASA Astrophysics Data System (ADS)

Colas, B.; Clark, S. M.; Jacob, D. E.

2015-12-01

Amorphous calcium carbonate (ACC) is a biogenic precursor of calcium carbonates forming shells and skeletons of marine organisms, which are key components of the whole marine environment. Understanding carbonate formation is an essential prerequisite to quantify the effect climate change and pollution have on marine population. Water is a critical component of the structure of ACC and the key component controlling the stability of the amorphous state. Addition of small amounts of magnesium (1-5% of the calcium content) is known to promote the stability of ACC presumably through stabilization of the hydrogen bonding network. Understanding the hydrogen bonding network in ACC is fundamental to understand the stability of ACC. Our approach is to use Monte-Carlo simulations constrained by X-ray and neutron scattering data to determine hydrogen bonding networks in ACC as a function of magnesium doping. We have already successfully developed a synthesis protocol to make ACC, and have collected X-ray data, which is suitable for determining Ca, Mg and O correlations, and have collected neutron data, which gives information on the hydrogen/deuterium (as the interaction of X-rays with hydrogen is too low for us to be able to constrain hydrogen atom positions with only X-rays). The X-ray and neutron data are used to constrain reverse Monte-Carlo modelling of the ACC structure using the Empirical Potential Structure Refinement program, in order to yield a complete structural model for ACC including water molecule positions. We will present details of our sample synthesis and characterization methods, X-ray and neutron scattering data, and reverse Monte-Carlo simulations results, together with a discussion of the role of hydrogen bonding in ACC stability.

Strong vibronic coupling effects in polarized IR spectra of the hydrogen bond in N-methylthioacetamide crystals

NASA Astrophysics Data System (ADS)

Flakus, Henryk T.; Śmiszek-Lindert, Wioleta; Stadnicka, Katarzyna

2007-06-01

This paper presents the investigation results of the polarized IR spectra of the hydrogen bond in crystals of N-methylthioacetamide. The spectral studies were preceded by the determination of the crystal X-ray structure. The spectra were measured at 283 K and at 77 K by a transmission method, using polarized light. Theoretical analysis of the results concerned the linear dichroic effects, the H/D isotopic and temperature effects, observed in the solid-state IR spectra of the hydrogen and of the deuterium bond at the frequency ranges of the νN-H and the νN-D bands, respectively. The main spectral properties of the crystals can be interpreted satisfactorily in terms of the simple quantitative theory of the IR spectra of the hydrogen bond, i.e., the " strong-coupling" theory on the basis of the hydrogen bond centrosymmetric dimer model. The spectra revealed that the strongest vibrational exciton coupling involved the closely spaced hydrogen bonds, each belonging to a different chain of associated N-methylthioacetamide molecules. The crystal spectral properties, along with an abnormal H/D isotopic effect in the spectra, were found to be strongly influenced by vibronic coupling mechanisms in these dimers. These mechanisms were considered as responsible for the activation in IR of the totally symmetric proton stretching vibrations in the dimers. On analyzing the spectra of isotopically diluted crystalline samples of N-methylthioacetamide, it was proved that a non-random distribution of the protons and deuterons took place in the hydrogen bond lattices. In an individual hydrogen-bonded chain in the crystals distribution of the hydrogen isotope atoms H and D was fully random. The H/D isotopic " self-organization" mechanism, of a vibronic nature, involved a pair of hydrogen bonds from a unit cell, where each hydrogen bond belonged to a different chain of the associated molecules.

Effects of hydrogen bond on the melting point of azole explosives

NASA Astrophysics Data System (ADS)

Wang, Jian-Hua; Shen, Chen; Liu, Yu-Cun; Luo, Jin; Duan, Yingjie

2018-07-01

Melting point is an important index to determine whether an explosive can be a melt cast carrier. In this study, the relationship among the molecular structure, crystal structure, and melting point of explosives was investigated by using nitroazole compounds. Hydrogen bonds influence crystal packing modes in chemically understandable ways. Hydrogen bonds also affect the changes in entropy and enthalpy in balancing melting process. Hence, different types of hydrogen bonds in explosive crystal structures were compared when the relationship between the molecular structure and the melting point of nitroazole explosives were analyzed. The effects of methyl and amino groups on intermolecular hydrogen bonds were also compared. Results revealed that the methyl and amino groups connected on the N(1) of the heterocyclic compound can reduce the melting point of azole explosive. This finding is possible because methyl and amino groups destroy the intermolecular hydrogen bond of the heterocyclic compound.

Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

PubMed Central

2016-01-01

Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

Hydrogen bonding in phytohormone-auxin (IAA) and its derivatives

NASA Astrophysics Data System (ADS)

Kojić-Prodić, Biserka; Kroon, Jan; Puntarec, Vitomir

1994-06-01

The significant importance of hydrogen bonds in biological structures and enzymatic reactions has been demonstrated in many examples. As a part of the molecular recognition study of auxins (plant growth hormones) the influence of hydrogen bonding on molecular conformation, particularly of the carboxyl group, which is one of the biologically active ligand sites, has been studied by X-ray diffraction and computational chemistry methods. The survey includes about 40 crystal structures of free auxins such as indol-3-ylacetic acid and its n-alkylated and halogenated derivatives but also bound auxins such as N-(indol-3-ylacetyl)- L-amino acids, and carbohydrate conjugates. The study includes hydrogen bonds of the NH⋯O and OH⋯O types. The classification of hydrogen bond patterns based on the discrimination between the centrosymmetric and non-centrosymmetric space groups and several examples of hydrogen bond systematics on graph set analysis are also shown.

Hydrogen bonds and twist in cellulose microfibrils.

PubMed

Kannam, Sridhar Kumar; Oehme, Daniel P; Doblin, Monika S; Gidley, Michael J; Bacic, Antony; Downton, Matthew T

2017-11-01

There is increasing experimental and computational evidence that cellulose microfibrils can exist in a stable twisted form. In this study, atomistic molecular dynamics (MD) simulations are performed to investigate the importance of intrachain hydrogen bonds on the twist in cellulose microfibrils. We systematically enforce or block the formation of these intrachain hydrogen bonds by either constraining dihedral angles or manipulating charges. For the majority of simulations a consistent right handed twist is observed. The exceptions are two sets of simulations that block the O2-O6' intrachain hydrogen bond, where no consistent twist is observed in multiple independent simulations suggesting that the O2-O6' hydrogen bond can drive twist. However, in a further simulation where exocyclic group rotation is also blocked, right-handed twist still develops suggesting that intrachain hydrogen bonds are not necessary to drive twist in cellulose microfibrils. Copyright © 2017 Elsevier Ltd. All rights reserved.

The mechanism of proton conduction in phosphoric acid

NASA Astrophysics Data System (ADS)

Vilčiauskas, Linas; Tuckerman, Mark E.; Bester, Gabriel; Paddison, Stephen J.; Kreuer, Klaus-Dieter

2012-06-01

Neat liquid phosphoric acid (H3PO4) has the highest intrinsic proton conductivity of any known substance and is a useful model for understanding proton transport in other phosphate-based systems in biology and clean energy technologies. Here, we present an ab initio molecular dynamics study that reveals, for the first time, the microscopic mechanism of this high proton conductivity. Anomalously fast proton transport in hydrogen-bonded systems involves a structural diffusion mechanism in which intramolecular proton transfer is driven by specific hydrogen bond rearrangements in the surrounding environment. Aqueous media transport excess charge defects through local hydrogen bond rearrangements that drive individual proton transfer reactions. In contrast, strong, polarizable hydrogen bonds in phosphoric acid produce coupled proton motion and a pronounced protic dielectric response of the medium, leading to the formation of extended, polarized hydrogen-bonded chains. The interplay between these chains and a frustrated hydrogen-bond network gives rise to the high proton conductivity.

Hydrogen bonding between hydrides of the upper-right part of the periodic table

NASA Astrophysics Data System (ADS)

Simončič, Matjaž; Urbic, Tomaz

2018-05-01

One of the most important electrostatic interactions between molecules is most definitely the hydrogen bond. Understanding the basis of this interaction may offer us the insight needed to understand its effect on the macroscopic scale. Hydrogen bonding is for example the reason for anomalous properties in compounds like water and naturally life as we know it. The strength of the bond depends on numerous factors, among them the electronegativity of participating atoms. In this work we calculated the strength of hydrogen bonds between hydrides of the upper-right part of the periodic table (C, N, O, F, P, S, Cl, As, Se, Br) using quantum-chemical methods. The aim was to determine what influences the strength of strong and weak hydrogen bonds in simple hydrides. Various relationships were checked. A relation between the strength of the bond and the electronegativity of the participating atoms was found. We also observed a correlation between the strength of hydrogen bonds and the inter-atomic distances, along with the dependence on the charge transfer on the atom of the donor. We also report characteristic geometries of different dimers.

Theoretical study of negatively charged Fe(-)-(H2O)(n ≤ 6) clusters.

PubMed

Castro, Miguel

2012-06-14

Interactions of a singly negatively charged iron atom with water molecules, Fe(-)-(H(2)O)(n≤6), in the gas phase were studied by means of density functional theory. All-electron calculations were performed using the B3LYP functional and the 6-311++G(2d,2p) basis set for the Fe, O, and H atoms. In the lowest total energy states of Fe(-)-(H(2)O)(n), the metal-hydrogen bonding is stronger than the metal-oxygen one, producing low-symmetry structures because the water molecules are directly attached to the metal by basically one of their hydrogen atoms, whereas the other ones are involved in a network of hydrogen bonds, which together with the Fe(δ-)-H(δ+) bonding accounts for the nascent hydration of the Fe(-) anion. For Fe(-)-(H(2)O)(3≤n), three-, four-, five-, and six-membered rings of water molecules are bonded to the metal, which is located at the surface of the cluster in such a way as to reduce the repulsion with the oxygen atoms. Nevertheless, internal isomers appear also, lying less than 3 or 5 kcal/mol for n = 2-3 or n = 4-6. These results are in contrast with those of classical TM(+)-(H(2)O)(n) complexes, where the direct TM(+)-O bonding usually produces high symmetry structures with the metal defining the center of the complex. They show also that the Fe(-) anions, as the TM(+) ions, have great capability for the adsorption of water molecules, forming Fe(-)-(H(2)O)(n) structures stabilized by Fe(δ-)-H(δ+) and H-bond interactions.

Design of ferrocene-dipeptide bioorganometallic conjugates to induce chirality-organized structures.

PubMed

Moriuchi, Toshiyuki; Hirao, Toshikazu

2010-07-20

The highly ordered molecular assemblies in proteins can have a variety of functions, as observed in enzymes, receptors, and the like. Synthetic scientists are constructing bioinspired systems by harnessing the self-assembling properties of short peptides. Secondary structures such as alpha-helices, beta-sheets, and beta-turns are important in protein folding, which is mostly directed and stabilized by hydrogen bonding and the hydrophobic interactions of side chains. The design of secondary structure mimics that are composed of short peptides has attracted much attention, both for gaining fundamental insight into the factors affecting protein folding and for developing pharmacologically useful compounds, artificial receptors, asymmetric catalysts, and new materials. Ferrocenes are an organometallic scaffold with a central reverse-turn unit based on the inter-ring spacing of about 3.3 A, which is a suitable distance for hydrogen bonding between attached peptide strands. The conjugation of organometallic compounds with biomolecules such as amino acids, peptides, and DNA should provide novel systems that reflect properties of both the ferrocene and the biologically derived moieties. In this Account, we focus on recent advances in the design of ferrocene-peptide bioconjugates, which help illustrate the peptidomimetic basis for protein folding and the means of constructing highly ordered molecular assemblies. Ferrocene-peptide bioconjugates are constructed to form chirality-organized structures in both solid and solution states. The ferrocene serves as a reliable organometallic scaffold for the construction of protein secondary structures via intramolecular hydrogen bonding: the attached dipeptide strands are constrained within the appropriate dimensions. The introduction of the chiral dipeptide chains into the ferrocene scaffold induces the conformational enantiomerization of the ferrocenyl moiety; the chirality-organized structure results from intramolecular hydrogen bonding. The configuration and sequence of the amino acids are instrumental in the process. Regulation of the directionality and specificity of hydrogen bonding is a key component in the design of various molecular assemblies. Ferrocene-peptide bioconjugates also have a strong tendency to self-assemble through the contributions of available hydrogen-bonding donors in the solid state. Some ferrocene-peptide bioconjugates bearing only one dipeptide chain exhibit a helically ordered molecular assembly through a network of intermolecular (rather than intramolecular) hydrogen bonds. The propensity to form the chiral helicity appears to be controlled by the chirality of the dipeptide chains. Organization of host molecules is a useful strategy for forming artificial receptors. The conformationally regulated ferrocene-peptide bioconjugate provides the chirality-organized binding site for size-selective and chiral recognition of dicarboxylic acids through multipoint hydrogen bonds. Metal ions serve a variety of purposes in proteins, including structural stabilization for biological function. The complexation of ferrocene-peptide bioconjugates with palladium(II) compounds not only stabilizes the chirality conformational regulation but also induces conformational regulation of the dipeptide chain through complexation and intramolecular chirality organization. Construction of the chirality-organized ferrocene-peptide bioconjugates is also achieved by metal-directed assembly. These varied examples amply demonstrate the value of ferrocene-peptide bioconjugates in asserting architectural control over highly ordered molecular assemblies.

Non-opioid analgesic drug flupirtine: Spectral analysis, DFT computations, in vitro bioactivity and molecular docking study

NASA Astrophysics Data System (ADS)

Leenaraj, D. R.; Hubert Joe, I.

2017-06-01

Spectral features of non-opioid analgesic drug flupirtine have been explored by the Fourier transform infrared, Raman and Nuclear magnetic resonance spectroscopic techniques combined with density functional theory computations. The bioactive conformer of flupirtine is stabilized by an intramolecular Csbnd H⋯N hydrogen bonding resulting by the steric strain of hydrogen atoms. Natural bond orbital and natural population analysis support this result. The charge redistribution also has been analyzed. Antimicrobial activities of flupirtine have been screened by agar well disc diffusion and molecular docking methods, which exposes the importance of triaminopyridine in flupirtine.

The role of hydrogen bonding in the fluorescence quenching of 2,6-bis((E)-2-(benzoxazol-2-yl)vinyl)naphthalene (BBVN) in methanol

NASA Astrophysics Data System (ADS)

Hammam, Essam; Basahi, Jalal; Ismail, Iqbal; Hassan, Ibrahim; Almeelbi, Talal

2017-02-01

The excited state hydrogen bonding dynamics of BBVN in hydrogen donating methanol solvent was explored at the TD-BMK/cc-pVDZ level of theory with accounting for the bulk environment effects at the polarizable continuum model (PCM). The heteroatoms of the BBVN laser dye form hydrogen bonds with four methanol molecules. In the formed BBVN-(MeOH)4 complex, the A-type hydrogen bond (N…HO), of an average strength of 25 kJ mol- 1, is twofold stronger than the B-type (O…HO) one. Upon photon absorption, the total HB binding energy increases from 78.5 kJ mol- 1 in the ground state to 82.6 kJ mol- 1 in the first singlet (S1) excited state. In consequence of the hydrogen bonding interaction, the absorption band maximum of the BBVN-(MeOH)4 complex, which was anticipated at 398 nm (exp. 397), is redshifted by 5 nm relative to that of the free dye in methanol. The spectral shift of the stretching vibrational mode for the hydrogen bonded hydroxyl groups (with a maximum shift of 285 cm- 1) from that of the free methanol indicated the elevated strengthening of hydrogen bonds in the excited state. The vibrational modes associated with hydrogen bonding provide effective accepting modes for the dissipation of the excitation energy, thus, decreasing the fluorescence quantum yield of BBVN in alcohols as compared to that in the polar aprotic solvents. Since there is no sign of photochemistry or phosphorescence, it seems reasonable in view of the outcomes of this study to assign the major decay process of the excited singlet (S1) of BBVN in alcohols to vibronically induced internal conversion (IC) facilitated by hydrogen bonding.

Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.

PubMed

Luo, Zhoujie; Gao, Ya; Zhu, Tong; Zhang, John Zenghui; Xia, Fei

2017-08-31

Water molecules can serve as proton shuttles for proton transfer in the C-H bond insertion reactions catalyzed by transition metal complexes. Recently, the control experiments performed for C-H bond insertion of phenol and anisol by gold carbenes show that large discrepancy exists in the yields of hydrogenated and deuterated products. Thus, we conducted a detailed theoretical analysis on the function of water molecules in the C-H bond insertion reactions. The comparison of calculated results and control experiments indicates that the solution water molecules play a crucial role of proton shuttle in C-H bond insertion. In particular, it was found that the hydroxyl groups in phenols were capable of donating protons via water shuttles for the production of C-H products, which had a substantial influence on the yields of inserted products. The hydroxyl groups instead of C-H bonds in phenols function like "proton reservoirs" in the C-H bond insertion, which we call the "proton self-sufficient" (PSS) function of phenol. The PSS function of phenol indicates that the substrates with and without proton reservoirs will lead to different C-H bond insertion products.

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli.

PubMed

Sun, Chang; Taguchi, Alexander T; Vermaas, Josh V; Beal, Nathan J; O'Malley, Patrick J; Tajkhorshid, Emad; Gennis, Robert B; Dikanov, Sergei A

2016-10-11

The respiratory cytochrome bo 3 ubiquinol oxidase from Escherichia coli has a high-affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQ H ), which is a transient intermediate during the electron-mediated reduction of O 2 to water. It is known that SQ H is stabilized by two strong hydrogen bonds from R71 and D75 to ubiquinone carbonyl oxygen O1 and weak hydrogen bonds from H98 and Q101 to O4. In this work, SQ H was investigated with orientation-selective Q-band (∼34 GHz) pulsed 1 H electron-nuclear double resonance (ENDOR) spectroscopy on fully deuterated cytochrome (cyt) bo 3 in a H 2 O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor T z' = 11.8 MHz, whereas for H2, T z' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (∼70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by ∼25°. Equilibrium molecular dynamics simulations on a membrane-embedded model of the cyt bo 3 Q H site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Density functional theory calculations support the idea that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone.

Observation of structure transition as a function of temperature in depositing hydrogenated sp2-rich carbon films

NASA Astrophysics Data System (ADS)

Wang, Yongfu; Gao, Kaixiong; Zhang, Junyan

2018-05-01

In this study, we carried out the transition experiments of graphite-like (GL) to fullerene-like (FL) structures by placing high temperature steel substrates in the depositing environment which can form FL hydrogenated carbon films. We investigated the changes of bond mixtures, H content, aromatic clusters and internal stress at the transition process, and proposed the transformation mechanism inferred from Raman, TEM cross-section, FTIR and XPS results. It was found that the size of aromatic clusters and accordingly graphene planes and the formation of edge dangling bonds were the key steps. H+ bombardment leaded to the splitting of large graphene planes (at GL stage) into more and smaller planes (at FL stage) and the formation of edge dangling bonds; Some of these dangling bonds were reduced by the formation of pentagons and subsequent curving of the smaller planes, which were an indicator of FL structures.

1,5-Bis[1-(2,4-dihy­droxy­phen­yl)ethyl­idene]carbonohydrazide dimethyl­formamide disolvate

PubMed Central

He, Qing-Peng; Tan, Bo; Lu, Ze-Hua

2010-01-01

In the title compound, C17H18N4O5·2C3H7NO, two solvent mol­ecules are linked to the main mol­ecule via N—H⋯O and O—H⋯O hydrogen bonds, forming a hydrogen-bonded trimer. Intra­molecular O—H⋯N hydrogen bonds influence the mol­ecular conformation of the main mol­ecule, and the two benzene rings form a dihedral angle of 10.55 (18)°. In the crystal, inter­molecular O—H⋯O hydrogen bonds link hydrogen-bonded trimers into ribbons extending along the b axis. PMID:21589135

Facile synthesis, single crystal analysis, and computational studies of sulfanilamide derivatives

NASA Astrophysics Data System (ADS)

Tahir, Muhammad Nawaz; Khalid, Muhammad; Islam, Ayesha; Ali Mashhadi, Syed Muddassir; Braga, Ataualpa A. C.

2017-01-01

Antibacterial resistance is a worldwide problem. Sulfanilamide is widely used antibacterial. For the first time, we report here a simple method for the derivative synthesis of the title drugs, single crystal XRD and density functional theory (DFT) studies. The optimized molecular structure, natural bond orbital (NBO), frontier molecular orbitals (FMOs) molecular electrostatic potential studies (MEP) and Mulliken population analysis (MPA) have been performed using M06-2X/6-31G(d, p). The FT-IR spectra and thermodynamic parameters were calculated at M06-2X/6-311 + G(2d,p) and B3LYP/6-31G(d, p) levels respectively, while, the UV-Vis analysis was performed using TD-DFT/B3LYP/6-31G(d, p) method. The experimental FT-IR spectra of both compounds were also carried out to reconfirm sbnd H⋯Osbnd hydrogen bonds. The DFT optimized parameters exhibiting good agreement with the experimental data. NBO analysis explored the hyper conjugative interaction and stability of title crystals, especially, reconfirmed the existence of sbnd H⋯Osbnd hydrogen bonds between the dimers. The FT-IR, thermodynamic parameters, MEP and MPA also revealed the hydrogen bonding detail is harmonious to XRD data. As a matter of the fact, the hydrogen bonding is a significant parameter for the understanding and design of molecular crystals, subsequently; it can also play a vital role in the supramolecular chemistry. Moreover, the global reactivity descriptors suggest that title compounds might be bioactive.

Sorption and solubility of ofloxacin and norfloxacin in water-methanol cosolvent.

PubMed

Peng, Hongbo; Li, Hao; Wang, Chi; Zhang, Di; Pan, Bo; Xing, Baoshan

2014-05-01

Prediction of the properties and behavior of antibiotics is important for their risk assessment and pollution control. Theoretical calculation was incorporated in our experimental study to investigate the sorption of ofloxacin (OFL) and norfloxacin (NOR) on carbon nanotubes and their solubilities in water, methanol, and their mixture. Sorption for OFL and NOR decreased as methanol volume fractions (fc) increased. But the log-linear cosolvency model could not be applied as a general model to describe the cosolvent effect on OFL and NOR sorption. We computed the bond lengths of possible hydrogen bonds between solute and solvent and the corresponding interaction energies using Density Functional Theory. The decreased OFL solubility with increased fc could be attributed to the generally stronger hydrogen bond between OFL and H2O than that between OFL and CH3OH. Solubility of NOR varied nonmonotonically with increasing fc, which may be understood from the stronger hydrogen bond of NOR-CH3OH than NOR-H2O at two important sites (-O18 and -O21). The interaction energies were also calculated for the solute surrounded by solvent molecules at all the possible hydrogen bond sites, but it did not match the solubility variations with fc for both chemicals. The difference between the simulated and real systems was discussed. Similar sorption but different solubility of NOR and OFL from water-methanol cosolvent suggested that sorbate-solvent interaction seems not control their sorption. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cocrystals of 6-propyl-2-thiouracil: N-H···O versus N-H···S hydrogen bonds.

PubMed

Tutughamiarso, Maya; Egert, Ernst

2011-11-01

In order to investigate the relative stability of N-H···O and N-H···S hydrogen bonds, we cocrystallized the antithyroid drug 6-propyl-2-thiouracil with two complementary heterocycles. In the cocrystal pyrimidin-2-amine-6-propyl-2-thiouracil (1/2), C(4)H(5)N(3)·2C(7)H(10)N(2)OS, (I), the `base pair' is connected by one N-H···S and one N-H···N hydrogen bond. Homodimers of 6-propyl-2-thiouracil linked by two N-H···S hydrogen bonds are observed in the cocrystal N-(6-acetamidopyridin-2-yl)acetamide-6-propyl-2-thiouracil (1/2), C(9)H(11)N(3)O(2)·2C(7)H(10)N(2)OS, (II). The crystal structure of 6-propyl-2-thiouracil itself, C(7)H(10)N(2)OS, (III), is stabilized by pairwise N-H···O and N-H···S hydrogen bonds. In all three structures, N-H···S hydrogen bonds occur only within R(2)(2)(8) patterns, whereas N-H···O hydrogen bonds tend to connect the homo- and heterodimers into extended networks. In agreement with related structures, the hydrogen-bonding capability of C=O and C=S groups seems to be comparable.

The nature of hydrogen-bonding interactions in nonsteroidal anti-inflammatory drugs revealed by polarized IR spectroscopy.

PubMed

Hachuła, Barbara

2018-01-05

The influence of hydrogen-bonding interactions in the solid phase on the IR spectroscopic pattern of the ν OH band of nonsteroidal anti-inflammatory drugs (NSAIDs) was studied experimentally by IR spectroscopy with the use of polarized light at two temperatures (293K and 77K) and in isotopic dilution. The neat and deuterated crystals of (S)-naproxen ((S)-NPX), (R)-flurbiprofen ((R)-FBP), (RS)-flurbiprofen ((RS)-FBP) and (RS)-ketoprofen ((RS)-KTP) were obtained by melt crystallization between the two squeezed CaF 2 plates. The vibrational spectra of selected α-aryl propionic acid derivatives (2APAs) reflected the characteristics of their hydrogen-bond networks, i.e., 2APAs were characterized by the chain ((S)-NPX, (R)-FBP) and by dimeric ((RS)-FBP, (RS)-KTP) arrangement of hydrogen bonds in the crystal lattice. Spectroscopic results showed that the interchain (through-space) exciton coupling, between two laterally-spaced hydrogen bonds, dominates in the crystals of four NSAIDs. The same exciton coupled hydrogen bonds were also responsible for the H/D isotopic recognition mechanism in the crystalline spectra of deuterated 2APAs. The presented spectral results may help to predict the hydrogen bond motifs in the crystalline NSAIDs, which structures are not yet known, based on their IR spectra of hydrogen bond in the crystals. Copyright © 2017 Elsevier B.V. All rights reserved.

Simulation of the effect of hydrogen bonds on water activity of glucose and dextran using the Veytsman model.

PubMed

De Vito, Francesca; Veytsman, Boris; Painter, Paul; Kokini, Jozef L

2015-03-06

Carbohydrates exhibit either van der Waals and ionic interactions or strong hydrogen bonding interactions. The prominence and large number of hydrogen bonds results in major contributions to phase behavior. A thermodynamic framework that accounts for hydrogen bonding interactions is therefore necessary. We have developed an extension of the thermodynamic model based on the Veytsman association theory to predict the contribution of hydrogen bonds to the behavior of glucose-water and dextran-water systems and we have calculated the free energy of mixing and its derivative leading to chemical potential and water activity. We compared our calculations with experimental data of water activity for glucose and dextran and found excellent agreement far superior to the Flory-Huggins theory. The validation of our calculations using experimental data demonstrated the validity of the Veytsman model in properly accounting for the hydrogen bonding interactions and successfully predicting water activity of glucose and dextran. Our calculations of the concentration of hydrogen bonds using the Veytsman model were instrumental in our ability to explain the difference between glucose and dextran and the role that hydrogen bonds play in contributing to these differences. The miscibility predictions showed that the Veytsman model is also able to correctly describe the phase behavior of glucose and dextran. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular recognition in poly(epsilon-caprolactone)-based thermoplastic elastomers.

PubMed

Wisse, Eva; Spiering, A J H; van Leeuwen, Ellen N M; Renken, Raymond A E; Dankers, Patricia Y W; Brouwer, Linda A; van Luyn, Marja J A; Harmsen, Martin C; Sommerdijk, Nico A J M; Meijer, E W

2006-12-01

The molecular recognition properties of the hydrogen bonding segments in biodegradable thermoplastic elastomers were explored, aiming at the further functionalization of these potentially interesting biomaterials. A poly(epsilon-caprolactone)-based poly(urea) 2 was synthesized and characterized in terms of mechanical properties, processibility and histocompatibility. Comparison of the data with those obtained from the structurally related poly(urethane urea) 1 revealed that the difference in hard segment structure does not significantly affect the potency for application as a biomaterial. Nevertheless, the small differences in hard block composition had a strong effect on the molecular recognition properties of the hydrogen bonding segments. High selectivity was found for poly(urea) 2 in which bisureidobutylene-functionalized azobenzene dye 3 was selectively incorporated while bisureidopentylene-functionalized azobenzene dye 4 was completely released. In contrast, the incorporation of both dyes in poly(urethane urea) 1 led in both cases to their gradual release in time. Thermal analysis of the polymers in combination with variable temperature infrared experiments indicated that the hard blocks in 1 showed a sharp melting point, whereas those in 2 showed a very broad melting trajectory. This suggests a more precise organization of the hydrogen bonding segments in the hard blocks of poly(urea) 2 compared to poly(urethane urea) 1 and explains the results from the molecular recognition experiments. Preliminary results revealed that a bisureidobutylene-functionalized GRGDS peptide showed more supramolecular interaction with the PCL-based poly(urea), containing the bisureidobutylene recognition unit, as compared to HMW PCL, lacking this recognition unit.

Carbon-Hydrogen Bond Activation in Hydridotris(pyrazolyl)borate Platinum(IV) Complexes:  Comparison of Density Functionals, Basis Sets, and Bonding Patterns.

PubMed

Vastine, Benjamin Alan; Webster, Charles Edwin; Hall, Michael B

2007-11-01

The reaction mechanism for the cycle beginning with the reductive elimination (RE) of methane from κ(3)-TpPt(IV)(CH3)2H (1) (Tp = hydridotris(pyrazolyl)borate) and subsequent oxidative addition (OA) of benzene to form finally κ(3)-TpPt(IV)(Ph)2H (19) was investigated by density functional theory (DFT). Two mechanistic steps are of particular interest, namely the barrier to C-H coupling (barrier 1 - Ba1) and the barrier to methane release (barrier 2 - Ba2). For 31 density functionals, the calculated values for Ba1 and Ba2 were benchmarked against the experimentally reported values of 26 (Ba1) and 35 (Ba2) kcal·mol(-1), respectively. Specifically, the values for Ba1 and Ba2, calculated at the B3LYP/double-ζ plus polarization level of theory, are 24.6 and 34.3 kcal·mol(-1), respectively. Overall, the best performing functional was BPW91 where the mae associated with the calculated values of the two barriers is 0.68 kcal·mol(-1). The calculated B3LYP values of Ba1 ranged between 20 and 26 kcal·mol(-1) for 12 effective core potential basis sets for platinum and 29 all-electron basis sets for the first row elements. Polarization functions for the first row elements were important for accurate values, but the addition of diffuse functions to non-hydrogen (+) and hydrogen atoms (++) had little effect on the calculated values. Basis set saturation was achieved with APNO basis sets utilized for first-row atoms. Bader's "Atoms in Molecules" was used to analyze the electron density of several complexes, and the electron density at the Pt-Nax bond critical point (trans to the active site for C-H coupling) varied over a wider range than any of the other Pt-N bonds.

High density liquid structure enhancement in glass forming aqueous solution of LiCl.

PubMed

Camisasca, G; De Marzio, M; Rovere, M; Gallo, P

2018-06-14

We investigate using molecular dynamics simulations the dynamical and structural properties of LiCl:6H 2 O aqueous solution upon supercooling. This ionic solution is a glass forming liquid of relevant interest in connection with the study of the anomalies of supercooled water. The LiCl:6H 2 O solution is easily supercooled and the liquid state can be maintained over a large decreasing temperature range. We performed simulations from ambient to 200 K in order to investigate how the presence of the salt modifies the behavior of supercooled water. The study of the relaxation time of the self-density correlation function shows that the system follows the prediction of the mode coupling theory and behaves like a fragile liquid in all the range explored. The analysis of the changes in the water structure induced by the salt shows that while the salt preserves the water hydrogen bonds in the system, it strongly affects the tetrahedral hydrogen bond network. Following the interpretation of the anomalies of water in terms of a two-state model, the modifications of the oxygen radial distribution function and the angular distribution function of the hydrogen bonds in water indicate that LiCl has the role of enhancing the high density liquid component of water with respect to the low density component. This is in agreement with recent experiments on aqueous ionic solutions.

Why Does Alkylation of the N-H Functionality within M/NH Bifunctional Noyori-Type Catalysts Lead to Turnover?

PubMed

Dub, Pavel A; Scott, Brian L; Gordon, John C

2017-01-25

Molecular metal/NH bifunctional Noyori-type catalysts are remarkable in that they are among the most efficient artificial catalysts developed to date for the hydrogenation of carbonyl functionalities (loadings up to ∼10 -5 mol %). In addition, these catalysts typically exhibit high C═O/C═C chemo- and enantioselectivities. This unique set of properties is traditionally associated with the operation of an unconventional mechanism for homogeneous catalysts in which the chelating ligand plays a key role in facilitating the catalytic reaction and enabling the aforementioned selectivities by delivering/accepting a proton (H + ) via its N-H bond cleavage/formation. A recently revised mechanism of the Noyori hydrogenation reaction (Dub, P. A. et al. J. Am. Chem. Soc. 2014, 136, 3505) suggests that the N-H bond is not cleaved but serves to stabilize the turnover-determining transition states (TDTSs) via strong N-H···O hydrogen-bonding interactions (HBIs). The present paper shows that this is consistent with the largely ignored experimental fact that alkylation of the N-H functionality within M/NH bifunctional Noyori-type catalysts leads to detrimental catalytic activity. The purpose of this work is to demonstrate that decreasing the strength of this HBI, ultimately to the limit of its complete absence, are conditions under which the same alkylation may lead to beneficial catalytic activity.

High density liquid structure enhancement in glass forming aqueous solution of LiCl

NASA Astrophysics Data System (ADS)

Camisasca, G.; De Marzio, M.; Rovere, M.; Gallo, P.

2018-06-01

We investigate using molecular dynamics simulations the dynamical and structural properties of LiCl:6H2O aqueous solution upon supercooling. This ionic solution is a glass forming liquid of relevant interest in connection with the study of the anomalies of supercooled water. The LiCl:6H2O solution is easily supercooled and the liquid state can be maintained over a large decreasing temperature range. We performed simulations from ambient to 200 K in order to investigate how the presence of the salt modifies the behavior of supercooled water. The study of the relaxation time of the self-density correlation function shows that the system follows the prediction of the mode coupling theory and behaves like a fragile liquid in all the range explored. The analysis of the changes in the water structure induced by the salt shows that while the salt preserves the water hydrogen bonds in the system, it strongly affects the tetrahedral hydrogen bond network. Following the interpretation of the anomalies of water in terms of a two-state model, the modifications of the oxygen radial distribution function and the angular distribution function of the hydrogen bonds in water indicate that LiCl has the role of enhancing the high density liquid component of water with respect to the low density component. This is in agreement with recent experiments on aqueous ionic solutions.

Environment-dependent conformation investigation of 3-amino-1,2,4-triazole (3-AT): Raman Spectroscopy and density functional theory

NASA Astrophysics Data System (ADS)

Meng, Shuang; Zhao, Yanying; Xue, Jiadan; Zheng, Xuming

2018-02-01

In the paper, diverse tautomers of 3-amino-1,2,4-triazole (3AT) in solid and polar solvent have been explored by FT-IR, FT-Raman and 488 nm Raman experiments combing with quantum chemical theoretical calculation using PCM solvent model and normal mode analysis. The vibrational spectra prefer the 3-amino-1,2,4-2H-triazole (2H-3AT) dimer in solid, while in a polar solvent 3AT is apt to the 3-amino-1,2,4-2H-triazole (2H-3AT) monomer. The significant wavenumber difference and Raman intensity patterns in solid and different solvents are induced by hydrogen bond perturbation along > NH ⋯ N ≤ hydrogen bonds on five-membered N-heterocyclic ring. The ground state proton transfer reaction mechanism along the five-membered N-heterocyclic ring is supported by intermolecular hydrogen bonding between 3AT and protonic solvent molecules.

Molecular Dynamic Simulation of Diffusion Coefficients for Alkanols in Supercritical CO2 1

NASA Astrophysics Data System (ADS)

Li, Zhiwei; Lai, Shuhui; Gao, Wei; Chen, Liuping

2018-07-01

The infinite dilution diffusion coefficients ( D 12) of methanol, ethanol, 1-propanol, 1-butanol and 1-pentanol in supercritical CO2 (scCO2) at 313.2 K and 10-16 MPa were simulated by molecular dynamics (MD) simulation. The microscopic structure was also analyzed by calculation of the radial distribution function, coordination number (CN) between the center mass of solute and solvent molecules, and the average number of hydrogen bonding of this system. In infinite dilute solution, the probability of forming hydrogen bond between alkanol molecules is greatly reduced relative to pure alkanol fluid, and the weak hydrogen bonds formed between alkanol and CO2 molecules. In general, this work provides a reliable simulation method for transfer properties of solutes in scCO2. The prediction data were provides for the design and development of chemical processing. The results are helpful for one to deeper understand the relationship between microscopic structures of fluid and its transfer properties.

Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide-protein interactions.

PubMed Central

Meyer, J. E.; Schulz, G. E.

1997-01-01

The crystal structure of the maltodextrin-specific porin from Salmonella typhimurium ligated with a maltotrioside at the pore eyelet is known at 2.4 A resolution. The three glucose units assume a conformation close to the natural amylose helix. The pore eyelet fits exactly the cross-section of a maltooligosaccharide chain and thus functions as a constraining orifice. The oligomer permeates the membrane by screwing along the amylose helix through this orifice. Because each glucose glides along the given helix, its interactions can be sampled at any point along the pathway. The interactions are mostly hydrogen bonds, but also contacts to aromatic rings at one side of the pore. We have derived the energy profile of a gliding maltooligosaccharide by following formation and breakage of hydrogen bonds and by assessing the saccharide-aromatics interactions from a statistical analysis of saccharide binding sites in proteins. The resulting profile indicates smooth permeation despite extensive hydrogen bonding at the orifice. PMID:9144780

Scaling Relations for Adsorption Energies on Doped Molybdenum Phosphide Surfaces

DOE PAGES

Fields, Meredith; Tsai, Charlie; Chen, Leanne D.; ...

2017-03-10

Molybdenum phosphide (MoP), a well-documented catalyst for applications ranging from hydrotreating reactions to electrochemical hydrogen evolution, has yet to be mapped from a more fundamental perspective, particularly in the context of transition-metal scaling relations. In this work, we use periodic density functional theory to extend linear scaling arguments to doped MoP surfaces and understand the behavior of the phosphorus active site. The derived linear relationships for hydrogenated C, N, and O species on a variety of doped surfaces suggest that phosphorus experiences a shift in preferred bond order depending on the degree of hydrogen substitution on the adsorbate molecule. Thismore » shift in phosphorus hybridization, dependent on the bond order of the adsorbate to the surface, can result in selective bond weakening or strengthening of chemically similar species. As a result, we discuss how this behavior deviates from transition-metal, sulfide, carbide, and nitride scaling relations, and we discuss potential applications in the context of electrochemical reduction reactions.« less

Comparison of Degrees of Potential-Energy-Surface Anharmonicity for Complexes and Clusters with Hydrogen Bonds

NASA Astrophysics Data System (ADS)

Kozlovskaya, E. N.; Doroshenko, I. Yu.; Pogorelov, V. E.; Vaskivskyi, Ye. V.; Pitsevich, G. A.

2018-01-01

Previously calculated multidimensional potential-energy surfaces of the MeOH monomer and dimer, water dimer, malonaldehyde, formic acid dimer, free pyridine-N-oxide/trichloroacetic acid complex, and protonated water dimer were analyzed. The corresponding harmonic potential-energy surfaces near the global minima were constructed for series of clusters and complexes with hydrogen bonds of different strengths based on the behavior of the calculated multidimensional potential-energy surfaces. This enabled the introduction of an obvious anharmonicity parameter for the calculated potential-energy surfaces. The anharmonicity parameter was analyzed as functions of the size of the analyzed area near the energy minimum, the number of points over which energies were compared, and the dimensionality of the solved vibrational problem. Anharmonicity parameters for potential-energy surfaces in complexes with strong, medium, and weak H-bonds were calculated under identical conditions. The obtained anharmonicity parameters were compared with the corresponding diagonal anharmonicity constants for stretching vibrations of the bridging protons and the lengths of the hydrogen bridges.

Pseudosymmetric fac-di­aqua­trichlorido[(di­methyl­phosphor­yl)methanaminium-κO]manganese(II)

PubMed Central

Reiss, Guido J.

2013-01-01

In the title compound, [Mn(C3H11NOP)Cl3(H2O)2], the MnII metal center has a distorted o­cta­hedral geometry, coordinated by the three chloride ligands showing a facial arrangement. Two water mol­ecules and the O-coordinated dpmaH cation [dpmaH = (di­methyl­phosphor­yl)methanaminium] complete the coordination sphere. Each complex mol­ecule is connected to its neighbours by O—H⋯Cl and N—H⋯Cl hydrogen bonds. Two of the chloride ligands and the two water ligands form a hydrogen-bonded polymeric sheet in the ab plane. Furthermore, these planes are connected to adjacent planes by hydrogen bonds from the aminium function of cationic dpmaH ligand. A pseudo-mirror plane perpendicular to the b axis in the chiral space group P21 is observed together with inversion twinning [ratio = 0.864 (5):0.136 (5)]. PMID:23723764

Temperature Dependence in the Terahertz Spectrum of Nicotinamide: Anharmonicity and Hydrogen-Bonded Network.

PubMed

Takahashi, Masae; Okamura, Nubuyuki; Fan, Xinyi; Shirakawa, Hitoshi; Minamide, Hiroaki

2017-04-06

We have investigated the terahertz-spectral property of nicotinamide focusing on the temperature dependence in the range of 14-300 K. We observed that almost all peaks in the terahertz spectrum of the nicotinamide crystal showed a remarkable shift with temperature, whereas the lowest-frequency peak at 34.8 cm -1 showed a negligible shift with temperature. By analyzing the terahertz spectrum with the dispersion-corrected density functional theory calculations, we found that the difference in the temperature dependence of the peak shift is well understood in terms of the presence/absence of stretching vibration of the intermolecular hydrogen bond in the mode and the change of cell parameters. The anharmonicity in the dissociation potential energy of very weak intermolecular hydrogen bonding causes the remarkable peak shift with temperature in the terahertz spectrum of nicotinamide. This finding suggests that the assignment and identification of peaks in the terahertz spectrum are systematically enabled by temperature-dependent measurements.

The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study.

PubMed

Tobi, Dror; Elber, Ron; Thirumalai, Devarajan

2003-03-01

The conformational equilibrium of a blocked valine peptide in water and aqueous urea solution is studied using molecular dynamics simulations. Pair correlation functions indicate enhanced concentration of urea near the peptide. Stronger hydrogen bonding of urea-peptide compared to water-peptide is observed with preference for helical conformation. The potential of mean force, computed using umbrella sampling, shows only small differences between urea and water solvation that are difficult to quantify. The changes in solvent structure around the peptide are explained by favorable electrostatic interactions (hydrogen bonds) of urea with the peptide backbone. There is no evidence for significant changes in hydrophobic interactions in the two conformations of the peptide in urea solution. Our simulations suggest that urea denatures proteins by preferentially forming hydrogen bonds to the peptide backbone, reducing the barrier for exposing protein residues to the solvent, and reaching the unfolded state. Copyright 2003 Wiley Periodicals, Inc. Biopolymers: 359-369, 2003

Water Hydrogen-Bonding Network Structure and Dynamics at Phospholipid Multibilayer Surface: Femtosecond Mid-IR Pump-Probe Spectroscopy.

PubMed

Kundu, Achintya; Błasiak, Bartosz; Lim, Joon-Hyung; Kwak, Kyungwon; Cho, Minhaeng

2016-03-03

The water hydrogen-bonding network at a lipid bilayer surface is crucial to understanding membrane structures and its functional activities. With a phospholipid multibilayer mimicking a biological membrane, we study the temperature dependence of water hydrogen-bonding structure, distribution, and dynamics at a lipid multibilayer surface using femtosecond mid-IR pump-probe spectroscopy. We observe two distinguished vibrational lifetime components. The fast component (0.6 ps) is associated with water interacting with a phosphate part, whereas the slow component (1.9 ps) is with bulk-like choline-associated water. With increasing temperature, the vibrational lifetime of phosphate-associated water remains constant though its relative fraction dramatically increases. The OD stretch vibrational lifetime of choline-bound water slows down in a sigmoidal fashion with respect to temperature, indicating a noticeable change of the water environment upon the phase transition. The water structure and dynamics are thus shown to be in quantitative correlation with the structural change of liquid multibilayer upon the gel-to-liquid crystal phase transition.

Structure-directing weak phosphoryl XH...O=P (X = C, N) hydrogen bonds in cyclic oxazaphospholidines and oxazaphosphinanes.

PubMed

van der Lee, A; Rolland, M; Marat, X; Virieux, D; Volle, J N; Pirat, J L

2008-04-01

The structures of six cyclic oxazaphospholidines and three cyclic oxazaphosphinanes have been determined and their supramolecular structures have been compared. The molecules differ with respect to the functional groups attached to the central five- or six-membered rings, but have one phosphoryl group in common. The predominant feature in the supramolecular structures is the existence of relatively weak intermolecular phosphoryl XH...O=P (X = C, N) hydrogen bonds, creating in nearly all cases linear zigzag or double molecular chains. The molecular chains are in general linked to each other via very weak CH...pi or usual hydrogen-bond interactions. A survey of the Cambridge Structural Database on similar XH...O=P interactions shows a very large flexibility of the XH...O angle, which is in agreement with the DFT calculation reported elsewhere. The strength of the XH...O=P interaction can therefore be considered as relatively weak to moderately strong, and is expected to play at least a role in the formation of secondary substructures.

Unusual para-substituent effects on the intramolecular hydrogen-bond in hydrazone-based switches.

PubMed

Su, Xin; Lõkov, Märt; Kütt, Agnes; Leito, Ivo; Aprahamian, Ivan

2012-11-04

A "V"-shaped Hammett plot shows that resonance-assisted hydrogen bonding does not dictate the strength of the intramolecular hydrogen bond in the E isomers of hydrazone-based switches because it involves an aromatic pyridyl ring.

Oxidative coupling of sp 2 and sp 3 carbon-hydrogen bonds to construct dihydrobenzofurans.

PubMed

Shi, Jiang-Ling; Wang, Ding; Zhang, Xi-Sha; Li, Xiao-Lei; Chen, Yu-Qin; Li, Yu-Xue; Shi, Zhang-Jie

2017-08-10

Metal-catalyzed cross-couplings provide powerful, concise, and accurate methods to construct carbon-carbon bonds from organohalides and organometallic reagents. Recent developments extended cross-couplings to reactions where one of the two partners connects with an aryl or alkyl carbon-hydrogen bond. From an economic and environmental point of view, oxidative couplings between two carbon-hydrogen bonds would be ideal. Oxidative coupling between phenyl and "inert" alkyl carbon-hydrogen bonds still awaits realization. It is very difficult to develop successful strategies for oxidative coupling of two carbon-hydrogen bonds owning different chemical properties. This article provides a solution to this challenge in a convenient preparation of dihydrobenzofurans from substituted phenyl alkyl ethers. For the phenyl carbon-hydrogen bond activation, our choice falls on the carboxylic acid fragment to form the palladacycle as a key intermediate. Through careful manipulation of an additional ligand, the second "inert" alkyl carbon-hydrogen bond activation takes place to facilitate the formation of structurally diversified dihydrobenzofurans.Cross-dehydrogenative coupling is finding increasing application in synthesis, but coupling two chemically distinct sites remains a challenge. Here, the authors report an oxidative coupling between sp 2 and sp 3 carbons by sequentially activating the more active aryl site followed by the alkyl position.

Thermodynamics and vibrational study of hydrogenated carbon nanotubes: A DFT study

NASA Astrophysics Data System (ADS)

Khalil, Rana M. Arif; Hussain, Fayyaz; Rana, Anwar Manzoor; Imran, Muhammad

2018-02-01

Thermodynamic stability of the hydrogenated carbon nanotubes has been explored in the chemisorption limit. Statistical physics and density functional theory calculations have been used to predict hydrogen release temperatures at standard pressure in zigzag and armchair carbon nanotubes. It is found that hydrogen release temperatures decrease with increase in diameters of hydrogenated zigzag carbon nanotubes (CNTs) but opposite trend is noted in armchair CNTs at standard pressure of 1 bar. The smaller diameter hydrogenated zigzag CNTs have large values of hydrogen release temperature due to the stability of Csbnd H bonds. The vibrational density of states for hydrogenated carbon nanotubes have been calculated to confirm the Csbnd H stretching mode caused by sp3 hybridization.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil.

PubMed

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2014-06-05

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2013-09-01

In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

Regioselective synthesis of C3 alkylated and arylated benzothiophenes

PubMed Central

Shrives, Harry J.; Fernández-Salas, José A.; Hedtke, Christin; Pulis, Alexander P.; Procter, David J.

2017-01-01

Benzothiophenes are heterocyclic constituents of important molecules relevant to society, including those with the potential to meet modern medical challenges. The construction of molecules would be vastly more efficient if carbon–hydrogen bonds, found in all organic molecules, can be directly converted into carbon–carbon bonds. In the case of elaborating benzothiophenes, functionalization of carbon–hydrogen bonds at carbon-number 3 (C3) is markedly more demanding than at C2 due to issues of regioselectivity (C3 versus C2), and the requirement of high temperatures, precious metals and the installation of superfluous directing groups. Herein, we demonstrate that synthetically unexplored but readily accessible benzothiophene S-oxides serve as novel precursors for C3-functionalized benzothiophenes. Employing an interrupted Pummerer reaction to capture and then deliver phenol and silane coupling partners, we have discovered a directing group-free method that delivers C3-arylated and -alkylated benzothiophenes with complete regioselectivity, under metal-free and mild conditions. PMID:28317882

Supramolecularly engineered perylene bisimide assemblies exhibiting thermal transition from columnar to multilamellar structures.

PubMed

Yagai, Shiki; Usui, Mari; Seki, Tomohiro; Murayama, Haruno; Kikkawa, Yoshihiro; Uemura, Shinobu; Karatsu, Takashi; Kitamura, Akihide; Asano, Atsushi; Seki, Shu

2012-05-09

Perylene 3,4:9,10-tetracarboxylic acid bisimide (PBI) was functionalized with ditopic cyanuric acid to organize it into complex columnar architectures through the formation of hydrogen-bonded supermacrocycles (rosette) by complexing with ditopic melamines possessing solubilizing alkoxyphenyl substituents. The aggregation study in solution using UV-vis and NMR spectroscopies showed the formation of extended aggregates through hydrogen-bonding and π-π stacking interactions. The cylindrical fibrillar nanostructures were visualized by microscopic techniques (AFM, TEM), and the formation of lyotropic mesophase was confirmed by polarized optical microscopy and SEM. X-ray diffraction study revealed that a well-defined hexagonal columnar (Col(h)) structure was formed by solution-casting of fibrillar assemblies. All of these results are consistent with the formation of hydrogen-bonded PBI rosettes that spontaneously organize into the Col(h) structure. Upon heating the Col(h) structure in the bulk state, a structural transition to a highly ordered lamellar (Lam) structure was observed by variable-temperature X-ray diffraction, differential scanning calorimetry, and AFM studies. IR study showed that the rearrangement of the hydrogen-bonding motifs occurs during the structural transition. These results suggest that such a striking structural transition is aided by the reorganization in the lowest level of self-organization, i.e., the rearrangement of hydrogen-bonded motifs from rosette to linear tape. A remarkable increase in the transient photoconductivity was observed by the flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements upon converting the Col(h) structure to the Lam structure. Transient absorption spectroscopy revealed that electron transfer from electron-donating alkoxyphenyl groups of melamine components to electron-deficient PBI moieties takes place, resulting in a higher probability of charge carrier generation in the Lam structure compared to the Col(h) structure.

High-level ab initio calculations for the four low-lying families of minima of (H2O)(20): 1. Estimates of MP2/CBS binding energies and comparison with empirical potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fanourgakis, Georgios S.; Apra, Edoardo; Xantheas, Sotiris S.

2004-08-08

We report estimates of complete basis set (CBS) limits at the second-order Møller-Plesset perturbation level of theory (MP2) for the binding energies of the lowest lying isomers within each of the four major families of minima of (H2O)20. These were obtained by performing MP2 calculations with the family of correlation-consistent basis sets up to quadruple zeta quality, augmented with additional diffuse functions (aug-cc-pVnZ, n=D, T, Q). The MP2/CBS estimates are: -200.1 kcal/mol (dodecahedron, 30 hydrogen bonds), -212.6 kcal/mol (fused cubes, 36 hydrogen bonds), -215.0 (face-sharing pentagonal prisms, 35 hydrogen bonds) and –217.9 kcal/mol (edge-sharing pentagonal prisms, 34 hydrogen bonds). Themore » energetic ordering of the various (H2O)20 isomers does not follow monotonically the number of hydrogen bonds as in the case of smaller clusters such as the different isomers of the water hexamer. The dodecahedron lies ca. 18 kcal/mol higher in energy than the most stable edge-sharing pentagonal prism isomer. The TIP4P, ASP-W4, TTM2-R, AMOEBA and TTM2-F empirical potentials also predict the energetic stabilization of the edge-sharing pentagonal prisms with respect to the dodecahedron, albeit they universally underestimate the cluster binding energies with respect to the MP2/CBS result. Among them, the TTM2-F potential was found to predict the absolute cluster binding energies to within < 1% from the corresponding MP2/CBS values, whereas the error for the rest of the potentials considered in this study ranges from 3-5%.« less

Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing.

PubMed

Patil, Rohan; Das, Suranjana; Stanley, Ashley; Yadav, Lumbani; Sudhakar, Akulapalli; Varma, Ashok K

2010-08-16

Weak intermolecular interactions such as hydrogen bonding and hydrophobic interactions are key players in stabilizing energetically-favored ligands, in an open conformational environment of protein structures. However, it is still poorly understood how the binding parameters associated with these interactions facilitate a drug-lead to recognize a specific target and improve drugs efficacy. To understand this, comprehensive analysis of hydrophobic interactions, hydrogen bonding and binding affinity have been analyzed at the interface of c-Src and c-Abl kinases and 4-amino substituted 1H-pyrazolo [3, 4-d] pyrimidine compounds. In-silico docking studies were performed, using Discovery Studio software modules LigandFit, CDOCKER and ZDOCK, to investigate the role of ligand binding affinity at the hydrophobic pocket of c-Src and c-Abl kinase. Hydrophobic and hydrogen bonding interactions of docked molecules were compared using LigPlot program. Furthermore, 3D-QSAR and MFA calculations were scrutinized to quantify the role of weak interactions in binding affinity and drug efficacy. The in-silico method has enabled us to reveal that a multi-targeted small molecule binds with low affinity to its respective targets. But its binding affinity can be altered by integrating the conformationally favored functional groups at the active site of the ligand-target interface. Docking studies of 4-amino-substituted molecules at the bioactive cascade of the c-Src and c-Abl have concluded that 3D structural folding at the protein-ligand groove is also a hallmark for molecular recognition of multi-targeted compounds and for predicting their biological activity. The results presented here demonstrate that hydrogen bonding and optimized hydrophobic interactions both stabilize the ligands at the target site, and help alter binding affinity and drug efficacy.

Optimized Hydrophobic Interactions and Hydrogen Bonding at the Target-Ligand Interface Leads the Pathways of Drug-Designing

PubMed Central

Stanley, Ashley; Yadav, Lumbani; Sudhakar, Akulapalli; Varma, Ashok K.

2010-01-01

Background Weak intermolecular interactions such as hydrogen bonding and hydrophobic interactions are key players in stabilizing energetically-favored ligands, in an open conformational environment of protein structures. However, it is still poorly understood how the binding parameters associated with these interactions facilitate a drug-lead to recognize a specific target and improve drugs efficacy. To understand this, comprehensive analysis of hydrophobic interactions, hydrogen bonding and binding affinity have been analyzed at the interface of c-Src and c-Abl kinases and 4-amino substituted 1H-pyrazolo [3, 4-d] pyrimidine compounds. Methodology In-silico docking studies were performed, using Discovery Studio software modules LigandFit, CDOCKER and ZDOCK, to investigate the role of ligand binding affinity at the hydrophobic pocket of c-Src and c-Abl kinase. Hydrophobic and hydrogen bonding interactions of docked molecules were compared using LigPlot program. Furthermore, 3D-QSAR and MFA calculations were scrutinized to quantify the role of weak interactions in binding affinity and drug efficacy. Conclusions The in-silico method has enabled us to reveal that a multi-targeted small molecule binds with low affinity to its respective targets. But its binding affinity can be altered by integrating the conformationally favored functional groups at the active site of the ligand-target interface. Docking studies of 4-amino-substituted molecules at the bioactive cascade of the c-Src and c-Abl have concluded that 3D structural folding at the protein-ligand groove is also a hallmark for molecular recognition of multi-targeted compounds and for predicting their biological activity. The results presented here demonstrate that hydrogen bonding and optimized hydrophobic interactions both stabilize the ligands at the target site, and help alter binding affinity and drug efficacy. PMID:20808434

Assessment of the adsorption mechanism of Flutamide anticancer drug on the functionalized single-walled carbon nanotube surface as a drug delivery vehicle: An alternative theoretical approach based on DFT and MD

NASA Astrophysics Data System (ADS)

Kamel, Maedeh; Raissi, Heidar; Morsali, Ali; Shahabi, Mahnaz

2018-03-01

In the present work, we have studied the drug delivery performance of the functionalized (5, 5) single-walled carbon nanotube with a carboxylic acid group for Flutamide anticancer drug in the gas phase as well as water solution by means of density functional theory calculations. The obtained results confirmed the energetic stability of the optimized geometries and revealed that the nature of drug adsorption on the functionalized carbon nanotube is physical. Our computations showed that the hydrogen bonding between active sites of Flutamide molecule and the carboxyl functional group of the nanotube plays a vital role in the stabilization of the considered configurations. The natural bond orbital analysis suggested that the functionalized nanotube plays the role of an electron donor and Flutamide molecule acts as an electron acceptor at the investigated complexes. In addition, molecular dynamics simulation is also utilized to investigate the effect of functionalized carbon nanotube chirality on the dynamic process of drug molecule adsorption on the nanotube surface. Simulation results demonstrated that drug molecules are strongly adsorbed on the functionalized nanotube surface with (10,5) chirality, as reflected by the most negative van der Waals interaction energy and a high number of hydrogen bonds between the functionalized nanotube and drug molecules.

Spectral analysis and DFT computations of the hydrogen bonded complex between 2,6-diaminopyridine with 2,6-dichloro-4-nitrophenol in different solvents

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Soliman, Saied M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2017-09-01

New hydrogen bonded complex between 2,6-dichloro-4-nitrophenol (DCNP), proton donor with the proton acceptor 2,6-diaminopyridine (DAP) has been synthesized and characterized in solution and solid state by different spectroscopic techniques. Electronic spectra were used to identify the novel proton transfer complex through appearance of new absorption bands in acetonitrile (CH3CN), methanol (CH3OH) and mixture composed from 1:1 methanol and acetonitrile (AN-Me). The complex stoichiometry was determined to be 1:1 by job's method and photometric titrations. The formation constant was determined by applying minimum-maximum absorbances method where it reached high values confirming the complex high stability. A spectroscopic method for determining DAP was presented and validated statistically. The solid complex was characterized by elemental analysis, infrared and 1H NMR studies where the hydrogen bonded reaction occurs between the phenolic OH with the pyridine ring nitrogen as well as one amino group of DNP. The density functional theory DFT (B3LYP) method has been used to energy optimization of the reactants and complex in the ground state using two basis sets 6-31G(d) and 6-31 G+(d,p). The first one led to energy optimized structure through bifurcated hydrogen bond between OH of DCNP with the ring nitrogen and one amino group of DAP with optimization energy -1998.7 Hartree. The second one gave an optimized structure thought hydrogen bonding between OH and one amino group with lowered optimization energy -2018.1 Hartree. Hence, the experimental results will be simulated with the most stable one at DFT/B3LYB 6-31G+ (d,p). The most reactive electrophilic and nucleophilic sites of DCNP and DAP were predicted using the molecular electrostatic potential. The theoretical electronic spectra in the gas phase and the investigated solvents were calculated at TD-DFT/B3LYP 6-31G+ (d,p) and compared with measured electronic spectra where a satisfactory results have been obtained. An important aim of this work is analysis of the interaction energies between the filled natural bond orbitals (NBOs) and the empty ones in order to shed the light on the ease of electron delocalization among bonds in the novel hydrogen bonded complex.

1,2,4,5-Benzenetetracarboxylic acid: a versatile hydrogen bonding template for controlling the regioselective topochemical synthesis of head-to-tail photodimers from stilbazole derivatives.

PubMed

Ortega, Gabriela; Hernández, Jesús; González, Teresa; Dorta, Romano; Briceño, Alexander

2018-05-16

The crystal engineering of hydrogen bonded organic assemblies based on 1,2,4,5-benzenetetracarboxylic acid (H4bta) and stilbazole derivatives (1-10) is exploited to provide regio-controlled [2 + 2] photocycloadditions in the solid state. Single crystal X-ray diffraction analyses have revealed that all the arrays are built-up from the self-assembly of the (H2bta)2- dianion with two stilbazolium cations via O-HO- and N+-HO- charge-assisted H-bonding synthons: (4-Hstilbazolium+)2(H2bta2-). The dianion displays an interesting diversity of H-bonding motifs. Such structural flexibility allowed us to obtain four structure-types defined by the preferential formation of intramolecular or intermolecular hydrogen bonds between carboxylate-carboxylic groups. In these ionic assemblies two predominant structural H-bonding patterns were observed. The first pattern is characterised by the formation of intramolecular H-bonds in the dianion, leading to discrete assemblies based on ternary arrays. The second hydrogen pattern consists of 2-D hydrogen networks built-up from the self-assembly of anions via intermolecular H-bonds that are linked to the cations. Two additional examples, in which the dianion is self-assembled in two types of ribbons, were also observed. Another supramolecular feature predominant in all these arrays is the stacking of the cations in a head-to-tail fashion, which is controlled via cation-π interactions. These arrays are photoactive in the solid state upon UV-irradiation leading to the regioselective synthesis of rctt-cyclobutane head-to-tail-isomers in high to quantitative yield. In this work, the template tolerance either to steric or electronic effects by changing the number or positions of the supramolecular interactions exerted by distinctive functional groups was also explored. In addition, assemblies bearing 2-chloro (7 and 8) and 3-chloro-4-stilbazole (1 and 9) crystallize in two different crystalline forms, leading to novel examples of supramolecular isomers with similar solid state reactivity.

Highly selective rhodium catalyzed domino C-H activation/cyclizations.

PubMed

Trans, Duc N; Cramer, Nicolai

2011-01-01

The direct functionalization of carbon-hydrogen bonds is an emerging tool to establish more sustainable and efficient synthetic methods. We present its implementation in a cascade reaction that provides a rapid assembly of functionalized indanylamines from simple and readily available starting materials. Careful choice of the ancillary ligand---an electron-rich bidentate phosphine ligand--enables highly diastereoselective rhodium(i)-catalyzed intramolecular allylations of unsubstituted ketimines induced by a directed C-H bond activation and allene carbo-metalation sequence.

Deactivation of 6-Aminocoumarin Intramolecular Charge Transfer Excited State through Hydrogen Bonding

PubMed Central

Krystkowiak, Ewa; Dobek, Krzysztof; Maciejewski, Andrzej

2014-01-01

This paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in various aprotic hydrogen-bond forming solvents. It was established that solvent polarity as well as hydrogen-bonding ability influence solute properties. The hydrogen-bonding interactions between S1-electronic excited solute and solvent molecules were found to facilitate the nonradiative deactivation processes. The energy-gap dependence on radiationless deactivation in aprotic solvents was found to be similar to that in protic solvents. PMID:25244014

Removal of distal protein–water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability

PubMed Central

Thomaeus, Ann; Naworyta, Agata; Mowbray, Sherry L.; Widersten, Mikael

2008-01-01

A putative proton wire in potato soluble epoxide hydrolase 1, StEH1, was identified and investigated by means of site-directed mutagenesis, steady-state kinetic measurements, temperature inactivation studies, and X-ray crystallography. The chain of hydrogen bonds includes five water molecules coordinated through backbone carbonyl oxygens of Pro186, Leu266, His269, and the His153 imidazole. The hydroxyl of Tyr149 is also an integrated component of the chain, which leads to the hydroxyl of Tyr154. Available data suggest that Tyr154 functions as a final proton donor to the anionic alkylenzyme intermediate formed during catalysis. To investigate the role of the putative proton wire, mutants Y149F, H153F, and Y149F/H153F were constructed and purified. The structure of the Y149F mutant was solved by molecular replacement and refined to 2.0 Å resolution. Comparison with the structure of wild-type StEH1 revealed only subtle structural differences. The hydroxyl group lost as a result of the mutation was replaced by a water molecule, thus maintaining a functioning hydrogen bond network in the proton wire. All mutants showed decreased catalytic efficiencies with the R,R-enantiomer of trans-stilbene oxide, whereas with the S,S-enantiomer, k cat/K M was similar or slightly increased compared with the wild-type reactions. k cat for the Y149F mutant with either TSO enantiomer was increased; thus the lowered enzyme efficiencies were due to increases in K M. Thermal inactivation studies revealed that the mutated enzymes were more sensitive to elevated temperatures than the wild-type enzyme. Hence, structural alterations affecting the hydrogen bond chain caused increases in k cat but lowered thermostability. PMID:18515642

Synthesis, Physicochemical Properties, and Hydrogen Bonding of 4(5)-Substituted 1-H-Imidazole-2-carboxamide, A Potential Universal Reader for DNA Sequencing by Recognition Tunneling

PubMed Central

Liang, Feng; Li, Shengqing

2012-01-01

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunnelling in nanopores.[1] The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH 6–10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC≫dT> dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied. PMID:22461259

Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability.

PubMed

Thomaeus, Ann; Naworyta, Agata; Mowbray, Sherry L; Widersten, Mikael

2008-07-01

A putative proton wire in potato soluble epoxide hydrolase 1, StEH1, was identified and investigated by means of site-directed mutagenesis, steady-state kinetic measurements, temperature inactivation studies, and X-ray crystallography. The chain of hydrogen bonds includes five water molecules coordinated through backbone carbonyl oxygens of Pro(186), Leu(266), His(269), and the His(153) imidazole. The hydroxyl of Tyr(149) is also an integrated component of the chain, which leads to the hydroxyl of Tyr(154). Available data suggest that Tyr(154) functions as a final proton donor to the anionic alkylenzyme intermediate formed during catalysis. To investigate the role of the putative proton wire, mutants Y149F, H153F, and Y149F/H153F were constructed and purified. The structure of the Y149F mutant was solved by molecular replacement and refined to 2.0 A resolution. Comparison with the structure of wild-type StEH1 revealed only subtle structural differences. The hydroxyl group lost as a result of the mutation was replaced by a water molecule, thus maintaining a functioning hydrogen bond network in the proton wire. All mutants showed decreased catalytic efficiencies with the R,R-enantiomer of trans-stilbene oxide, whereas with the S,S-enantiomer, k (cat)/K (M) was similar or slightly increased compared with the wild-type reactions. k (cat) for the Y149F mutant with either TSO enantiomer was increased; thus the lowered enzyme efficiencies were due to increases in K (M). Thermal inactivation studies revealed that the mutated enzymes were more sensitive to elevated temperatures than the wild-type enzyme. Hence, structural alterations affecting the hydrogen bond chain caused increases in k (cat) but lowered thermostability.

On the effects of basis set truncation and electron correlation in conformers of 2-hydroxy-acetamide

NASA Astrophysics Data System (ADS)

Szarecka, A.; Day, G.; Grout, P. J.; Wilson, S.

Ab initio quantum chemical calculations have been used to study the differences in energy between two gas phase conformers of the 2-hydroxy-acetamide molecule that possess intramolecular hydrogen bonding. In particular, rotation around the central C-C bond has been considered as a factor determining the structure of the hydrogen bond and stabilization of the conformer. Energy calculations include full geometiy optimization using both the restricted matrix Hartree-Fock model and second-order many-body perturbation theory with a number of commonly used basis sets. The basis sets employed ranged from the minimal STO-3G set to [`]split-valence' sets up to 6-31 G. The effects of polarization functions were also studied. The results display a strong basis set dependence.

Quantum mechanics models of the methanol dimer: OH⋯O hydrogen bonds of β-d-glucose moieties from crystallographic data.

PubMed

Cintrón, Michael Santiago; Johnson, Glenn P; French, Alfred D

2017-04-18

The interaction of two methanol molecules, simplified models of carbohydrates and cellulose, was examined using a variety of quantum mechanics (QM) levels of theory. Energy plots for hydrogen bonding distance (H⋯O) and angle (OH⋯O) were constructed. All but two experimental structures were located in stabilized areas on the vacuum phase energy plots. Each of the 399 models was analyzed with Bader's atoms-in-molecules (AIM) theory, which showed a widespread ability by the dimer models to form OH⋯O hydrogen bonds that have bond paths and Bond Critical Points. Continuum solvation calculations suggest that a portion of the energy-stabilized structures could occur in the presence of water. A survey of the Cambridge Structural Database (CSD) for all donor-acceptor interactions in β-D-glucose moieties examined the similarities and differences among the hydroxyl groups and acetal oxygen atoms that participate in hydrogen bonds. Comparable behavior was observed for the O2H, O3H, O4H, and O6H hydroxyls, acting either as acceptors or donors. Ring O atoms showed distinct hydrogen bonding behavior that favored mid-length hydrogen bonds. Published by Elsevier Ltd.

Water: two liquids divided by a common hydrogen bond.

PubMed

Soper, Alan K

2011-12-08

The structure of water is the subject of a long and ongoing controversy. Unlike simpler liquids, where atomic interactions are dominated by strong repulsive forces at short distances and weaker attractive (van der Waals) forces at longer distances, giving rise to local atomic coordination numbers of order 12, water has pronounced and directional hydrogen bonds which cause the dense liquid close-packed structure to open out into a disordered and dynamic network, with coordination number 4-5. Here I show that water structure can be accurately represented as a mixture of two identical, interpenetrating, molecular species separated by common hydrogen bonds. Molecules of one type can form hydrogen bonds with molecules of the other type but cannot form hydrogen bonds with molecules of the same type. These hydrogen bonds are strong along the bond but weak with respect to changes in the angle between neighboring bonds. The observed pressure and temperature dependence of water structure and thermodynamic properties follow naturally from this choice of water model, and it also gives a simple explanation of the enduring claims based on spectroscopic evidence that water is a mixture of two components. © 2011 American Chemical Society

A hydrogen-bonding network modulating enzyme function: asparagine-194 and tyrosine-225 of Escherichia coli aspartate aminotransferase.

PubMed

Yano, T; Mizuno, T; Kagamiyama, H

1993-02-23

The electron distribution within the coenzyme or coenzyme-substrate conjugate needs to be properly regulated during the catalytic process of aspartate aminotransferase (AspAT). Asn194 and Tyr225 may function in regulating the electron distribution through hydrogen-bonding to O(3') of the coenzyme, pyridoxal 5'-phosphate (PLP) or pyridoxamine 5'-phosphate (PMP). The roles of Tyr225 have already been explored by site-directed mutagenesis (Inoue et al., 1991; Goldberg et al., 1991). In the present studies, the mutant enzymes Asn194-->Ala and Asn194-->Ala + Tyr225-->Phe were analyzed kinetically and spectroscopically and were compared with the wild-type and Tyr225-->Phe enzymes. The kinetic studies showed that Asn194 is not essential for AspAT catalysis, although the Kd values for the substrates were increased by 10- to 50-fold upon the replacement of Asn194. The measurements of the absorption and fluorescence excitation spectra revealed that the ratio of an enolimine to a ketoenamine form was considerably increased as a tautomeric form of the protonated PLP in the active site of the double mutant enzyme. The pH-pKd relationship for the binding of maleate to AspAT could be explained by a simple thermodynamic cycle where only one ionizing group (the imine nitrogen of the internal aldimine bond) affects the binding of maleate. The analyses of the pH-pKd curves for the wild-type and mutant enzymes showed that (i) the hydrogen bond between O(3') of PLP and Asn194 is weakened by the binding of maleate to AspAT, while the hydrogen bond between O(3') and Tyr225 is not changed, and that (ii) the replacement of Asn194 causes some effect hampering the binding of maleate.(ABSTRACT TRUNCATED AT 250 WORDS)

Multiple hydrogen bonds. Mass spectra of hydrogen bonded heterodimers. A comparison of ESI- and REMPI-ReTOF-MS.

PubMed

Taubitz, Jörg; Lüning, Ulrich; Grotemeyer, Jürgen

2004-11-07

Resonance enhanced multi-photon ionization-reflectron time of flight mass spectrometry is the analytical method of choice to observe hydrogen bonded supramolecules in the gas phase when protonation of basic centers competes with cluster formation.

Hydrogen-bonded supramolecular structures of three related 4-(5-nitro-2-furyl)-1,4-dihydropyridines.

PubMed

Quesada, Antonio; Argüello, Jacqueline; Squella, Juan A; Wardell, James L; Low, John N; Glidewell, Christopher

2006-01-01

In ethyl 5-cyano-2,6-dimethyl-4-(5-nitro-2-furyl)-1,4-dihydropyridine-3-carboxylate, C15H15N3O5, the molecules are linked into chains by a single N-H...O hydrogen bond. The molecules in diethyl 2,6-dimethyl-4-(5-nitro-2-furyl)-1,4-dihydropyridine-3,5-dicarboxylate, C17H20N2O7, are linked by a combination of one N-H...O hydrogen bond and two C-H...O hydrogen bonds into sheets built from equal numbers of R(2)(2)(17) and R(4)(4)(18) rings. In 2,6-dimethyl-4-(5-nitro-2-furyl)-1,4-dihydropyridine-3,5-dicarbonitrile, C13H10N4O3, the molecules are linked by a combination of a three-centre N-H...(O)2 hydrogen bond and two independent two-centre C-H...O hydrogen bonds into complex sheets containing four types of ring.

Hydrogen bonding effects on the reorganization energy for photoinduced charge separation reaction between porphyrin and quinone studied by nanosecond laser flash photolysis.

PubMed

Yago, Tomoaki; Gohdo, Masao; Wakasa, Masanobu

2010-02-25

Alcohol concentration dependences of photoinduced charge separation (CS) reaction of zinc tetraphenyl-porphyrin (ZnTPP) and duroquinone (DQ) were investigated in benzonitrile by a nanosecond laser flash photolysis technique. The photoinduced CS reaction was accelerated by the addition of alcohols, whereas the addition of acetonitrile caused little effect on the CS reactions. The simple theory was developed to calculate an increase in reorganization energies induced by the hydrogen bonding interactions between DQ and alcohols using the chemical equilibrium constants for the hydrogen bonding complexes through the concerted pathway and the stepwise one. The experimental results were analyzed by using the Marcus equation where we took into account the hydrogen bonding effects on the reorganization energy and the reaction free energy for the CS reaction. The observed alcohol concentration dependence of the CS reaction rates was well explained by the formation of the hydrogen bonding complexes through the concerted pathway, demonstrating the increase in the reorganization energy by the hydrogen bonding interactions.

Mapping the force field of a hydrogen-bonded assembly

NASA Astrophysics Data System (ADS)

Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2014-05-01

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Molecular interactions in the betaine monohydrate-polyol deep eutectic solvents: Experimental and computational studies

NASA Astrophysics Data System (ADS)

Zahrina, Ida; Mulia, Kamarza; Yanuar, Arry; Nasikin, Mohammad

2018-04-01

DES (deep eutectic solvents) are a new class of ionic liquids that have excellent properties. The strength of interaction between molecules in the DES affects their properties and applications. In this work, the strength of molecular interactions between components in the betaine monohydrate salt and polyol (glycerol or/and propylene glycol) eutectic mixtures was studied by experimental and computational studies. The melting point and fusion enthalpy of the mixtures were measured using STA (Simultaneous Thermal Analyzer). The nature and strength of intermolecular interactions were observed by FT-IR and NMR spectroscopy. The molecular dynamics simulation was used to determine the number of H-bonds, percent occupancy, and radial distribution functions in the eutectic mixtures. The interaction between betaine monohydrate and polyol is following order: betaine monohydrate-glycerol-propylene glycol > betaine monohydrate-glycerol > betaine monohydrate-propylene glycol, where the latter is the eutectic mixture with the lowest stability, strength and extent of the hydrogen bonding interactions between component molecules. The presence of intra-molecular hydrogen bonding interactions, the inter-molecular hydrogen bonding interactions between betaine molecule and polyol, and also interactions between polyol and H2O of betaine monohydrate in the eutectic mixtures.

X-ray Diffraction and Density Functional Theory Provide Insight into Vanadate Binding to Homohexameric Bromoperoxidase II and the Mechanism of Bromide Oxidation.

PubMed

Radlow, Madlen; Czjzek, Mirjam; Jeudy, Alexandra; Dabin, Jerome; Delage, Ludovic; Leblanc, Catherine; Hartung, Jens

2018-05-18

X-ray diffraction of native bromoperoxidase II (EC 1.11.1.18) from the brown alga Ascophyllum nodosum reveals at a resolution of 2.26 Å details of orthovanadate binding and homohexameric protein organization. Three dimers interwoven in contact regions and tightened by hydrogen-bond-clamped guanidinium stacks along with regularly aligned water molecules form the basic structure of the enyzme. Intra- and intermolecular disulfide bridges further stabilize the enzyme preventing altogether the protein from denaturing up to a temperature of 90 °C, as evident from dynamic light scattering and the on-gel ortho-dianisidine assay. Every monomer binds one equivalent of orthovanadate in a cavity formed from side chains of three histidines, two arginines, one lysine, serine, and tryptophan. Protein binding occurs primarily through hydrogen bridges and superimposed by Coulomb attraction according to thermochemical model on density functional level of theory (B3LYP/6-311++G**). The strongest attractor is the arginine side chain mimic N-methylguanidinium, enhancing in positive cooperative manner hydrogen bridges toward weaker acceptors, such as residues from lysine and serine. Activating hydrogen peroxide occurs in the thermochemical model by side-on binding in orthovanadium peroxoic acid, oxidizing bromide with virtually no activation energy to hydrogen bonded hypobromous acid.

Hydrogenated amorphous silicon formation by flux control and hydrogen effects on the growth mechanism

NASA Astrophysics Data System (ADS)

Toyoda, H.; Sugai, H.; Kato, K.; Yoshida, A.; Okuda, T.

1986-06-01

The composition of particle flux to deposit hydrogenated amorphous silicon films in a glow discharge is controlled by a combined electrostatic-magnetic deflection technique. As a result, the films are formed firstly without hydrogen ion flux, secondly by neutral flux only, and thirdly by all species fluxes. Comparison of these films reveals the significant role of hydrogen in the surface reactions. Hydrogen breaks the Si-Si bond, decreases the sticking probability of the Si atom, and replaces the SiH bond by a SiH2 bond to increase the hydrogen content of the films.

The effect of pressure on the hydration structure around hydrophobic solute: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Sarma, Rahul; Paul, Sandip

2012-03-01

Molecular dynamics simulations are performed to study the effects of pressure on the hydrophobic interactions between neopentane molecules immersed in water. Simulations are carried out for five different pressure values ranging from 1 atm to 8000 atm. From potential of mean force calculations, we find that with enhancement of pressure, there is decrease in the well depth of contact minimum (CM) and the relative stability of solvent separated minimum over CM increases. Lower clustering of neopentane at high pressure is also observed in association constant and cluster-structure analysis. Selected site-site radial distribution functions suggest efficient packing of water molecules around neopentane molecules at elevated pressure. The orientational profile calculations of water molecules show that the orientation of water molecules in the vicinity of solute molecule is anisotropic and this distribution becomes flatter as we move away from the solute. Increasing pressure slightly changes the water distribution. Our hydrogen bond properties and dynamics calculations reveal pressure-induced formation of more and more number of water molecules with five and four hydrogen bond at the expense of breaking of two and three hydrogen bonded water molecules. We also find lowering of water-water continuous hydrogen bond lifetime on application of pressure. Implication of these results for relative dispersion of hydrophobic molecules at high pressure are discussed.

Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy.

PubMed

Vöhringer-Martinez, E; Link, O; Lugovoy, E; Siefermann, K R; Wiederschein, F; Grubmüller, H; Abel, B

2014-09-28

Supercritical water and methanol have recently drawn much attention in the field of green chemistry. It is crucial to an understanding of supercritical solvents to know their dynamics and to what extent hydrogen (H) bonds persist in these fluids. Here, we show that with femtosecond infrared (IR) laser pulses water and methanol can be heated to temperatures near and above their critical temperature Tc and their molecular dynamics can be studied via ultrafast photoelectron spectroscopy at liquid jet interfaces with high harmonics radiation. As opposed to previous studies, the main focus here is the comparison between the hydrogen bonded systems of methanol and water and their interpretation by theory. Superheated water initially forms a dense hot phase with spectral features resembling those of monomers in gas phase water. On longer timescales, this phase was found to build hot aggregates, whose size increases as a function of time. In contrast, methanol heated to temperatures near Tc initially forms a broad distribution of aggregate sizes and some gas. These experimental features are also found and analyzed in extended molecular dynamics simulations. Additionally, the simulations enabled us to relate the origin of the different behavior of these two hydrogen-bonded liquids to the nature of the intermolecular potentials. The combined experimental and theoretical approach delivers new insights into both superheated phases and may contribute to understand their different chemical reactivities.

Molecular structure and vibrational assignment of dimethyl oxaloacetate

NASA Astrophysics Data System (ADS)

Tayyari, Sayyed Faramarz; Salemi, Sirous; Tabrizi, Mansoureh Zahedi; Behforouz, Mohammad

2004-06-01

A complete conformational analysis of the keto and chelated enol forms of dimethyl oxaloacetate (DMOA), a β-dicarbonyl compound, was carried out by ab initio calculations, at the density functional theory (DFT) level. In addition to nine stable enol conformers, which are stabilized by intramolecular hydrogen bonds, twelve stable keto conformers were also obtained. The considerably higher energy of the keto compared to that of the most stable enol conformer makes the presence of keto form, at least in the gas phase, unlikely. Theoretical calculations in the solution, using the Onsager Method, suggest two coexisting enol conformers in the solution. This finding is in agreement with the experimental data. The hydrogen bond strength of the most stable conformer of DMOA is compared with that of acetylacetone (AA). Harmonic vibrational frequencies of this stable enol form and its deuterated analog were also calculated and compared with the experimental data. According to the theoretical calculations, the enolated proton in dimethyl oxaloacetate moves in an asymmetric single minimum potential with a hydrogen bond strength of 31.1 kJ/mol, 35.3 kJ/mol less than that of AA. This weakening of hydrogen bond is consistent with the frequency shifts for OH/OD stretching, OH/OD out-of-plane bending and O⋯O stretching modes. The calculated O ⋯O distance is about 0.07-0.08 Å longer than that of its parent AA.

Conformational analysis, tautomerization, IR, Raman, and NMR studies of benzyl acetoacetate

NASA Astrophysics Data System (ADS)

Tayyari, Sayyed Faramarz; Naghavi, Farnaz; Pojhan, Sahar; McClurg, Ryan W.; Sammelson, Robert E.

2011-02-01

A complete conformational analysis of the keto and enol forms of benzyl acetoacetate (BAA), a β-dicarbonyl compound, was carried out by ab initio calculations, at the density functional theory (DFT) level. By inspection of all possible conformers and tautomers, 22 stable cis-enol, 28 stable trans-enol, and five keto conformers were obtained. Among all stable cis-enol forms only six of them are engaged in intramolecular hydrogen bond. The hydrogen bond strength of the most stable conformer of BAA is compared with that of acetylacetone (AA) and dimethyl oxaloacetate (DMOA). Harmonic vibrational frequencies of the most stable enol and keto forms and their deuterated analogues were also calculated and compared with the experimental data. According to the theoretical calculations, the hydrogen bond strength of the most stable enol conformer of BAA is 56.7 kJ/mol (calculated at the B3LYP/6-311++G ∗∗ level), about 10 kJ/mol less than that of AA. This weakening of hydrogen bond is consistent with the spectroscopic results. NMR studies indicate that BAA exists mainly as a keto tautomer in all considered solutions. The Gibbs energies for keto/enol tautomerization were calculated at the B3LYP level, with several basis sets, in both gas phase and CH 3CN solution (using PCM model), for the most stable enol and keto conformers.

NMR investigation and theoretical calculations of the solvent effect on the conformation of valsartan

NASA Astrophysics Data System (ADS)

Chashmniam, Saeed; Tafazzoli, Mohsen

2017-11-01

Structure and conformational properties of valsartan were studied by advanced NMR techniques and quantum calculation methods. Potential energy scanning using B3LYP/6-311++g** and B3LYP-D3/6-311++g** methods were performed and four conformers (V1-V4) at minimum points of PES diagram were observed. According to the NMR spectra in acetone-d6, there are two conformers (M and m) with m/M = 0.52 ratio simultaneously and energy barriers of the two conformers were predicted from chemical shifts and multiplicities. While, intramolecular hydrogen bond at tetrazole ring and carboxylic groups prevent the free rotation on N6sbnd C11 bond in M-conformer, this bond rotates freely in m-conformer. On the other hand, intramolecular hydrogen bond at carbonyl and carboxylic acid can be observed at m-conformer. So, different intramolecular hydrogen bond is the reason for the stability of both M and m structures. Quite interestingly, 1H NMR spectra in CDCl3 show two distinct conformers (N and n) with unequal ratio which are differ from M-m conformers. Also, intramolecular hydrogen bond seven-member ring involving five-membered tetrazole ring and carboxylic acid group observed in both N and n-conformers Solvent effect, by using a set of polar and non-polar solvents including DMSO-d6, methanol-d4, benzene-d6, THF-d8, nitromethane-d3, methylene chloride-d2 and acetonitrile-d3 were investigated. NMR parameters include chemical shifts and spin-spin coupling constants were obtained from a set of 2D NMR spectra (H-H COSY, HMQC and HMBC). For this purpose, several DFT functionals from LDA, GGA and hybrid categories were used which the hybrid method showed better agreement with experiment values.

Expeditious diastereoselective synthesis of elaborated ketones via remote Csp3-H functionalization

NASA Astrophysics Data System (ADS)

Shu, Wei; Lorente, Adriana; Gómez-Bengoa, Enrique; Nevado, Cristina

2017-01-01

The quest for selective C-H functionalization reactions, able to provide new strategic opportunities for the rapid assembly of molecular complexity, represents a major focus of the chemical community. Examples of non-directed, remote Csp3-H activation to forge complex carbon frameworks remain scarce due to the kinetic stability and thus intrinsic challenge associated to the chemo-, regio- and stereoselective functionalization of aliphatic C-H bonds. Here we describe a radical-mediated, directing-group-free regioselective 1,5-hydrogen transfer of unactivated Csp3-H bonds followed by a second Csp2-H functionalization to produce, with exquisite stereoselectivity, a variety of elaborated fused ketones. This study demonstrates that aliphatic acids can be strategically harnessed as 1,2-diradical synthons and that secondary aliphatic C-H bonds can be engaged in stereoselective C-C bond-forming reactions, highlighting the potential of this protocol for target-oriented natural product and pharmaceutical synthesis.

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo

2016-06-13

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and vanmore » der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.« less

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

PubMed

Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

2016-09-01

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

A Computational and Theoretical Study of Conductance in Hydrogen-bonded Molecular Junctions

NASA Astrophysics Data System (ADS)

Wimmer, Michael

This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano-junctions between molecular electronic devices and biological systems. This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junction significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction. In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH˙˙˙O, OH˙˙˙O, and NH˙˙˙N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has focused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance descriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular description of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions. A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.

Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization.

PubMed

Reddy, Th Dhileep N; Mallik, Bhabani S

2017-04-19

This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site-site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of the charged entities, cations and anions, in the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic conductivities and hydrogen bonds as well as residence dynamics. The diffusion coefficients and ionic conductivity decrease with an increase in the size of the cation or anion. The effect of alkyl chain length on ionic conductivity calculated in this article is consistent with the findings of other experimental studies. Hydrogen bond lifetimes and residence times along with structure factors were also calculated, and are related to alkyl chain length.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Senesi, Roberto; Flammini, Davide; Kolesnikov, Alexander I.

The OH stretching vibrational spectrum of water was measured in a wide range of temperatures across the triple point, 269 K < T < 296 K, using Inelastic Neutron Scattering (INS). The hydrogen projected density of states and the proton mean kinetic energy, _OH, were determined for the first time within the framework of a harmonic description of the proton dynamics. We found that in the liquid the value of _OH is nearly constant as a function of T, indicating that quantum effects on the OH stretching frequency are weakly dependent on temperature. In the case of ice, ab initiomore » electronic structure calculations, using non-local van der Waals functionals, provided _OH values in agreement with INS experiments. We also found that the ratio of the stretching (_OH) to the total (_exp) kinetic energy, obtained from the present measurements, increases in going from ice, where hydrogen bonding is the strongest, to the liquid at ambient conditions and then to the vapour phase, where hydrogen bonding is the weakest. The same ratio was also derived from the combination of previous deep inelastic neutron scattering data, which does not rely upon the harmonic approximation, and the present measurements. We found that the ratio of stretching to the total kinetic energy shows a minimum in the metastable liquid phase. This finding suggests that the strength of intermolecular interactions increases in the supercooled phase, with respect to that in ice, contrary to the accepted view that supercooled water exhibits weaker hydrogen bonding than ice.« less

Poly(sebacoyl diglyceride) Cross-Linked by Dynamic Hydrogen Bonds: A Self-Healing and Functionalizable Thermoplastic Bioelastomer.

PubMed

Chen, Shuo; Bi, Xiaoping; Sun, Lijie; Gao, Jin; Huang, Peng; Fan, Xianqun; You, Zhengwei; Wang, Yadong

2016-08-17

Biodegradable and biocompatible elastomers (bioelastomers) could resemble the mechanical properties of extracellular matrix and soft tissues and, thus, are very useful for many biomedical applications. Despite significant advances, tunable bioelastomers with easy processing, facile biofunctionalization, and the ability to withstand a mechanically dynamic environment have remained elusive. Here, we reported new dynamic hydrogen-bond cross-linked PSeD-U bioelastomers possessing the aforementioned features by grafting 2-ureido-4[1H]-pyrimidinones (UPy) units with strong self-complementary quadruple hydrogen bonds to poly(sebacoyl diglyceride) (PSeD), a refined version of a widely used bioelastomer poly(glycerol sebacate) (PGS). PSeD-U polymers exhibited stronger mechanical strength than their counterparts of chemically cross-linked PSeD and tunable elasticity by simply varying the content of UPy units. In addition to the good biocompatibility and biodegradability as seen in PSeD, PSeD-U showed fast self-healing (within 30 min) at mild conditions (60 °C) and could be readily processed at moderate temperature (90-100 °C) or with use of solvent casting at room temperature. Furthermore, the free hydroxyl groups of PSeD-U enabled facile functionalization, which was demonstrated by the modification of PSeD-U film with FITC as a model functional molecule.

Hydrogen bonds and antiviral activity of benzaldehyde derivatives

NASA Astrophysics Data System (ADS)

Tolstorozhev, G. B.; Skornyakov, I. V.; Belkov, M. V.; Shadyro, O. I.; Brinkevich, S. D.; Samovich, S. N.

2012-09-01

We have obtained the Fourier transform IR spectra of solutions of benzaldehyde derivatives having different antiviral activities against a herpes virus. We observe a correlation between the presence of hydrogen bonds in the benzaldehyde molecules and the appearance of antiviral properties in the compounds. For compounds having antiviral activity, we have obtained spectral data suggesting the existence of hydrogen bonds of the type C=OṡṡṡH-O and O-HṡṡṡO in the molecules. When the hydrogen atom in the hydroxyl groups are replaced by a methyl group, no intramolecular hydrogen bonds are formed and the compounds lose their antiviral activity.

Structual Effects of Cytidine 2^' Ribose Modifications as Determined by Irmpd Action Spectroscopy

NASA Astrophysics Data System (ADS)

Hamlow, Lucas; He, Chenchen; Fan, Lin; Wu, Ranran; Yang, Bo; Rodgers, M. T.; Berden, Giel; Oomens, J.

2015-06-01

Modified nucleosides, both naturally occurring and synthetic play an important role in understanding and manipulating RNA and DNA. Naturally occurring modified nucleosides are commonly found in functionally important regions of RNA and also affect antibiotic resistance or sensitivity. Synthetic modifications of nucleosides such as fluorinated and arabinosyl nucleosides have found uses as anti-virals and chemotherapy agents. Understanding the effect that modifications have on structure and glycosidic bond stability may lend insight into the functions of these modified nucleosides. Modifications such as the naturally occurring 2^'-O-methylation and the synthetic 2^'-fluorination are believed to help stabilize the nucleoside through the glycosidic bond stability and intramolecular hydrogen bonding. Changing the sugar from ribose to arabinose alters the stereochemistry at the 2^' position and thus shifts the 3D orientation of the 2^'-hydroxyl group, which also affects intramolecular hydrogen bonding and glycosidic bond stability. The structures of 2^'-deoxy-2^'-fluorocytidine, 2^'-O-methylcytidine and cytosine arabinoside are examined in the current work by measuring the infrared spectra in the IR fingerprint region using infrared multiple photon dissociation (IRMPD) action spectroscopy. The structures accessed in the experiments were determined via comparison of the measured IRMPD action spectra to the theoretical linear IR spectra determined by density functional theory and molecular modeling for the stable low-energy structures. Although glycosidic bond stability cannot be quantitatively determined from this data, complementary TCID studies will establish the effect of these modifications. Comparison of these modified nucleosides with their RNA and DNA analogues will help elucidate differences in their intrinsic chemistry.

Quantum nature of protons in water probed by scanning tunneling microscopy and spectroscopy

NASA Astrophysics Data System (ADS)

Guo, Jing; Lü, Jing-Tao; Feng, Yexin; Chen, Ji; Peng, Jinbo; Lin, Zeren; Meng, Xiangzhi; Wang, Zhichang; Li, Xin-Zheng; Wang, En-Ge; Jiang, Ying; Jing-Tao Lü Team; Xin-Zheng Li Team

The complexity of hydrogen-bonding interaction largely arises from the quantum nature of light hydrogen nuclei, which has remained elusive for decades. Here we report the direct assessment of nuclear quantum effects on the strength of a single hydrogen bond formed at a water-salt interface, using tip-enhanced inelastic electron tunneling spectroscopy (IETS) based on a low-temperature scanning tunneling microscope (STM). The IETS signals are resonantly enhanced by gating the frontier orbitals of water via a chlorine-terminated STM tip, such that the hydrogen-bonding strength can be determined with unprecedentedly high accuracy from the redshift in the O-H stretching frequency of water. Isotopic substitution experiments combined with quantum simulations reveal that the anharmonic quantum fluctuations of hydrogen nuclei weaken the weak hydrogen bonds and strengthen the relatively strong ones. However, this trend can be completely reversed when the hydrogen bond is strongly coupled to the polar atomic sites of the surface.

Towards the synthesis of prenylated phloroglucinol derivatives: An X-ray crystallographic and DFT study of unexpected reaction products

NASA Astrophysics Data System (ADS)

Akerman, Matthew P.; Mkhize, Zimbili; van Heerden, Fanie R.

2018-07-01

Owing to their bioactivity and prevalence in medicinal plant extracts, prenylated phloroglucinols have garnered significant interest. Towards the synthesis of prenylated phloroglucinol derivatives, 2,4,6-trihydroxy-3-(3-methylbut-2-enyl)acetophenone is required as an intermediate. Herein, this was synthesised by a tandem Claisen-Cope rearrangement reaction on 2,4-bis(methoxymethoxy)-6-(3-methylbut-2-enyloxy)acetophenone and a subsequent hydrolysis to remove protecting groups. This reaction yielded the desired product as well as three by-products. Two of these by-products were isomeric chromane derivatives (2 and 3) and the third was a methoxy derivative (4). These compounds have been studied by single crystal X-ray crystallography and DFT methods. Compound (2) crystallised in the P21/c space group with two hydrogen-bonded molecules in the asymmetric unit (Z = 8). Compound (4) crystallised in the Pbca space group with a single molecule in the asymmetric unit (Z = 8). Both compounds formed extensive supramolecular structures supported by hydrogen bonds in the solid state. Compound (2) forms a simple one-dimensional hydrogen-bonded chain co-linear with the a-axis. Compound (4) forms a two-dimensional supramolecular structure comprising "pentameric" hydrogen-bonded motifs linked by additional H-bonds to form the supramolecular structure. Both structures showed intramolecular hydrogen bonds between the acetyl oxygen and adjacent OH group. DFT simulations were used to probe the relative energies of the molecules and hydrogen bonds. These simulations showed that the intramolecular hydrogen bond has a substantial stabilising effect with an interaction strength of 70.64 kJ mol-1. The formation of the hydrogen-bonded dimer of (2) from which the supramolecular structure is formed has a ΔHassoc constant of -42.32 kJ mol-1, illustrating that the formation of the hydrogen-bonded structure is energetically favourable.

The role of hydrogen bonding in the fluorescence quenching of 2,6-bis((E)-2-(benzoxazol-2-yl)vinyl)naphthalene (BBVN) in methanol.

PubMed

Hammam, Essam; Basahi, Jalal; Ismail, Iqbal; Hassan, Ibrahim; Almeelbi, Talal

2017-02-15

The excited state hydrogen bonding dynamics of BBVN in hydrogen donating methanol solvent was explored at the TD-BMK/cc-pVDZ level of theory with accounting for the bulk environment effects at the polarizable continuum model (PCM). The heteroatoms of the BBVN laser dye form hydrogen bonds with four methanol molecules. In the formed BBVN-(MeOH) 4 complex, the A-type hydrogen bond (N…HO), of an average strength of 25kJmol -1 , is twofold stronger than the B-type (O…HO) one. Upon photon absorption, the total HB binding energy increases from 78.5kJmol -1 in the ground state to 82.6kJmol -1 in the first singlet (S 1 ) excited state. In consequence of the hydrogen bonding interaction, the absorption band maximum of the BBVN-(MeOH) 4 complex, which was anticipated at 398nm (exp. 397), is redshifted by 5nm relative to that of the free dye in methanol. The spectral shift of the stretching vibrational mode for the hydrogen bonded hydroxyl groups (with a maximum shift of 285cm -1 ) from that of the free methanol indicated the elevated strengthening of hydrogen bonds in the excited state. The vibrational modes associated with hydrogen bonding provide effective accepting modes for the dissipation of the excitation energy, thus, decreasing the fluorescence quantum yield of BBVN in alcohols as compared to that in the polar aprotic solvents. Since there is no sign of photochemistry or phosphorescence, it seems reasonable in view of the outcomes of this study to assign the major decay process of the excited singlet (S 1 ) of BBVN in alcohols to vibronically induced internal conversion (IC) facilitated by hydrogen bonding. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular mechanism of gelation with ethylene glycol added to a solution of polyacrylonitrile in dimethylsulfoxide

NASA Astrophysics Data System (ADS)

Vettegren', V. I.; Machalaba, N. N.; Zharov, V. B.; Kulik, V. B.; Savitskii, A. V.

2011-06-01

The mechanism of solidifying a solution of polyacrylonitrile (PAN) in dimethylsulfoxide (DMSO) into which ethylene glycol is added is studied by the method of Raman spectroscopy. In the absence of ethylene glycol, DMSO molecules produce dipole-dipole bonds to PAN molecules. Upon adding ethylene glycol, DMSO molecules form hydrogen bonds with it and a line at 1000 cm-1 appears in the Raman spectrum, which is assigned to the valence vibrations of S=O bonds involved in the hydrogen bonds. After DMSO is removed, ethylene glycol molecules produce hydrogen bonds with two neighboring PAN molecules, giving rise to a band at 2264 cm-1, which is assigned to the valence vibrations of C≡N bonds involved in these hydrogen bonds. A high-viscosity gel consisting of PAN molecules arises in which these molecules are bonded to each other through ethylene glycol molecules.

Biomimetic Self-Healing

DTIC Science & Technology

2015-07-21

typically degrade quickly and are not capable of forming new bonds. In the 1930s it was already found that vulcanized rubber could self - heal in the...To overcome this limitation, Diesendruck et al. demonstrated Scheme 1. Mechanochemical scission and self - healing in vulcanized rubber . Long-lived...effective autonomic self - healing for soft materials. Cordier et al. prepared supramolecular rubbers based on hydrogen bonding between urea-functionalized

Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble

NASA Astrophysics Data System (ADS)

Zheng, Lixin; Chen, Mohan; Sun, Zhaoru; Ko, Hsin-Yu; Santra, Biswajit; Dhuvad, Pratikkumar; Wu, Xifan

2018-04-01

We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient approximation (GGA) functional approximation and carry out systematic comparisons with the results obtained from the GGA-level Perdew-Burke-Ernzerhof (PBE) functional and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band gaps, and dipole moments. We find that the SCAN functional is generally more accurate than the other two functionals for liquid water by not only capturing the intermediate-range vdW interactions but also mitigating the overly strong hydrogen bonds prescribed in PBE simulations. We also compare the results of SCAN-based AIMD simulations in the canonical and isothermal-isobaric ensembles. Our results suggest that SCAN provides a reliable description for most structural, electronic, and dynamical properties in liquid water.

Methanol clusters (CH3OH)n, n = 3-6 in external electric fields: density functional theory approach.

PubMed

Rai, Dhurba; Kulkarni, Anant D; Gejji, Shridhar P; Pathak, Rajeev K

2011-07-14

Structural evolution of cyclic and branched-cyclic methanol clusters containing three to six molecules, under the influence of externally applied uniform static electric field is studied within the density functional theory. Akin to the situation for water clusters, the electric field is seen to stretch the intermolecular hydrogen bonds, and eventually break the H-bonded network at certain characteristic threshold field values of field strength in the range 0.009-0.016 a.u., yielding linear or branched structures with a lower energy. These structural transitions are characterized by an abrupt increase in the electric dipole moment riding over its otherwise steady nonlinear increase with the applied field. The field tends to rupture the H-bonded structure; consequently, the number of hydrogen bonds decreases with increasing field strength. Vibrational spectra analyzed for fields applied perpendicular to the cyclic ring structures bring out the shifts in the OH ring vibrations (blueshift) and the CO stretch vibrations (redshift). For a given field strength, the blueshifts increase with the number of molecules in the ring and are found to be generally larger than those in the corresponding water cluster counterparts.

Hydrogen bonds in the vicinity of the special pair of the bacterial reaction center probed by hydrostatic high-pressure absorption spectroscopy.

PubMed

Kangur, Liina; Jones, Michael R; Freiberg, Arvi

2017-12-01

Using the native bacteriochlorophyll a pigment cofactors as local probes, we investigated the response to external hydrostatic high pressure of reaction center membrane protein complexes from the photosynthetic bacterium Rhodobacter sphaeroides. Wild-type and engineered complexes were used with a varied number (0, 1 or 2) of hydrogen bonds that bind the reaction center primary donor bacteriochlorophyll cofactors to the surrounding protein scaffold. A pressure-induced breakage of hydrogen bonds was established for both detergent-purified and membrane-embedded reaction centers, but at rather different pressures: between 0.2 and 0.3GPa and at about 0.55GPa, respectively. The free energy change associated with the rupture of the single hydrogen bond present in wild-type reaction centers was estimated to be equal to 13-14kJ/mol. In the mutant with two symmetrical hydrogen bonds (FM197H) a single cooperative rupture of the two bonds was observed corresponding to an about twice stronger bond, rather than a sequential rupture of two individual bonds. Copyright © 2017 Elsevier B.V. All rights reserved.

Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding?

PubMed Central

2017-01-01

Halogens are present in a significant number of drugs, contributing favorably to ligand–protein binding. Currently, the contribution of halogens, most notably chlorine and bromine, is largely attributed to halogen bonds involving favorable interactions with hydrogen bond acceptors. However, we show that halogens acting as hydrogen bond acceptors potentially make a more favorable contribution to ligand binding than halogen bonds based on quantum mechanical calculations. In addition, bioinformatics analysis of ligand–protein crystal structures shows the presence of significant numbers of such interactions. It is shown that interactions between halogens and hydrogen bond donors (HBDs) are dominated by perpendicular C–X···HBD orientations. Notably, the orientation dependence of the halogen–HBD (X–HBD) interactions is minimal over greater than 100° with favorable interaction energies ranging from −2 to −14 kcal/mol. This contrasts halogen bonds in that X–HBD interactions are substantially more favorable, being comparable to canonical hydrogen bonds, with a smaller orientation dependence, such that they make significant, favorable contributions to ligand–protein binding and, therefore, should be actively considered during rational ligand design. PMID:28657759

pi-Turns: types, systematics and the context of their occurrence in protein structures

PubMed Central

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-01-01

Background For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue γ-turn to six-residue π-turn. The Schellman motif occurring at the C-terminal end of α-helices is a classical example of hydrogen bonded π-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded β- and α-turns have been identified previously; likewise, a systematic characterization of π-turns would provide valuable insight into turn structures. Results An analysis of protein structures indicates that at least 20% of π-turns occur independent of the Schellman motif. The two categories of π-turns, designated as π-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length β- and α-turns, π-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal Cα-atoms, and this resulted in a comparable number of non-hydrogen-bonded π-turns (π-NHB). The presence of shorter β- and α-turns within all categories of π-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. Conclusion π-turns have been characterized, first using hydrogen bond and the distance between Cα atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the π-HB turns, being located on surface cavities, have functional role and there is also sequence conservation. PMID:18808671

pi-Turns: types, systematics and the context of their occurrence in protein structures.

PubMed

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-09-22

For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue gamma-turn to six-residue pi-turn. The Schellman motif occurring at the C-terminal end of alpha-helices is a classical example of hydrogen bonded pi-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded beta- and alpha-turns have been identified previously; likewise, a systematic characterization of pi-turns would provide valuable insight into turn structures. An analysis of protein structures indicates that at least 20% of pi-turns occur independent of the Schellman motif. The two categories of pi-turns, designated as pi-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length beta- and alpha-turns, pi-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal C alpha-atoms, and this resulted in a comparable number of non-hydrogen-bonded pi-turns (pi-NHB). The presence of shorter beta- and alpha-turns within all categories of pi-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. pi-turns have been characterized, first using hydrogen bond and the distance between C alpha atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the pi-HB turns, being located on surface cavities, have functional role and there is also sequence conservation.

Theoretical studies on photoelectron and IR spectral properties of Br2.-(H2O)n clusters.

PubMed

Pathak, A K; Mukherjee, T; Maity, D K

2007-07-28

We report vertical detachment energy (VDE) and IR spectra of Br2.-.(H2O)n clusters (n=1-8) based on first principles electronic structure calculations. Cluster structures and IR spectra are calculated at Becke's half-and-half hybrid exchange-correlation functional (BHHLYP) with a triple split valence basis function, 6-311++G(d,p). VDE for the hydrated clusters is calculated based on second order Moller-Plesset perturbation (MP2) theory with the same set of basis function. On full geometry optimization, it is observed that conformers having interwater hydrogen bonding among solvent water molecules are more stable than the structures having double or single hydrogen bonded structures between the anionic solute, Br2.-, and solvent water molecules. Moreover, a conformer having cyclic interwater hydrogen bonded network is predicted to be more stable for each size hydrated cluster. It is also noticed that up to four solvent H2O units can reside around the solute in a cyclic interwater hydrogen bonded network. The excess electron in these hydrated clusters is localized over the solute atoms. Weighted average VDE is calculated for each size (n) cluster based on statistical population of the conformers at 150 K. A linear relationship is obtained for VDE versus (n+3)(-1/3) and bulk VDE of Br2.- aqueous solution is calculated as 10.01 eV at MP2 level of theory. BHHLYP density functional is seen to make a systematic overestimation in VDE values by approximately 0.5 eV compared to MP2 data in all the hydrated clusters. It is observed that hydration increases VDE of bromine dimer anion system by approximately 6.4 eV. Calculated IR spectra show that the formation of Br2.--water clusters induces large shifts from the normal O-H stretching bands of isolated water keeping bending modes rather insensitive. Hydrated clusters, Br2.-.(H2O)n, show characteristic sharp features of O-H stretching bands of water in the small size clusters.

Theoretical studies on photoelectron and IR spectral properties of Br2.-(H2O)n clusters

NASA Astrophysics Data System (ADS)

Pathak, A. K.; Mukherjee, T.; Maity, D. K.

2007-07-01

We report vertical detachment energy (VDE) and IR spectra of Br2•-•(H2O)n clusters (n=1-8) based on first principles electronic structure calculations. Cluster structures and IR spectra are calculated at Becke's half-and-half hybrid exchange-correlation functional (BHHLYP) with a triple split valence basis function, 6-311++G(d,p). VDE for the hydrated clusters is calculated based on second order Moller-Plesset perturbation (MP2) theory with the same set of basis function. On full geometry optimization, it is observed that conformers having interwater hydrogen bonding among solvent water molecules are more stable than the structures having double or single hydrogen bonded structures between the anionic solute, Br2•-, and solvent water molecules. Moreover, a conformer having cyclic interwater hydrogen bonded network is predicted to be more stable for each size hydrated cluster. It is also noticed that up to four solvent H2O units can reside around the solute in a cyclic interwater hydrogen bonded network. The excess electron in these hydrated clusters is localized over the solute atoms. Weighted average VDE is calculated for each size (n) cluster based on statistical population of the conformers at 150K. A linear relationship is obtained for VDE versus (n+3)-1/3 and bulk VDE of Br2•- aqueous solution is calculated as 10.01eV at MP2 level of theory. BHHLYP density functional is seen to make a systematic overestimation in VDE values by ˜0.5eV compared to MP2 data in all the hydrated clusters. It is observed that hydration increases VDE of bromine dimer anion system by ˜6.4eV. Calculated IR spectra show that the formation of Br2•--water clusters induces large shifts from the normal O-H stretching bands of isolated water keeping bending modes rather insensitive. Hydrated clusters, Br2•-•(H2O)n, show characteristic sharp features of O-H stretching bands of water in the small size clusters.

Hydrogen bonding and spin density distribution in the QB semiquinone of bacterial reaction centers and comparison with the QA site

PubMed Central

Martin, Erik; Samoilova, Rimma I.; Narasimhulu, Kupala V.; Lin, Tzu-Jen; O’Malley, Patrick J.; Wraight, Colin A.; Dikanov, Sergei A.

2011-01-01

In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (QA) and secondary (QB) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the QA and QB sites, using samples of 15N-labeled reaction centers, with the native high spin Fe2+ exchanged for diamagnetic Zn2+, prepared in 1H2O and 2H2O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the QA SQ by Flores et al. (Biophys. J. 2007, 92, 671–682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6–5.4 MHz. HYSCORE was then applied to the QB SQ where we found proton lines corresponding to T~5.2, 3.7 MHz and T~1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the QB site, were used to assign the observed couplings to specific hydrogen bonding interactions with the QB SQ. These calculations allow us to assign the T=5.2 MHz proton to the His-L190 NδH…O4 (carbonyl) hydrogen bonding interaction. The T =3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the QB site show less asymmetric distribution of unpaired spin density over the SQ than seen for the QA site, consistent with available experimental data for 13C and 17O carbonyl hyperfine couplings. The implications of these interactions for QB function and comparisons with the QA site are discussed. PMID:21417328

Crystal structure of hydrocortisone acetate, C23H32O6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaduk, James A.; Gindhart, Amy M.; Blanton, Thomas N.

The crystal structure of hydrocortisone acetate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Hydrocortisone acetate crystallizes in space groupP2 1(#4) witha= 8.85173(3) Å,b= 13.53859(3) Å,c= 8.86980(4) Å,β= 101.5438(3)°,V= 1041.455(6) Å 3, andZ= 2. Both hydroxyl groups form hydrogen bonds to the ketone oxygen atom on the steroid ring system, resulting in a three-dimensional hydrogen bond network. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™.

Analysis of polarization in hydrogen bonded complexes: An asymptotic projection approach

NASA Astrophysics Data System (ADS)

Drici, Nedjoua

2018-03-01

The asymptotic projection technique is used to investigate the polarization effect that arises from the interaction between the relaxed, and frozen monomeric charge densities of a set of neutral and charged hydrogen bonded complexes. The AP technique based on the resolution of the original Kohn-Sham equations can give an acceptable qualitative description of the polarization effect in neutral complexes. The significant overlap of the electron densities, in charged and π-conjugated complexes, impose further development of a new functional, describing the coupling between constrained and non-constrained electron densities within the AP technique to provide an accurate representation of the polarization effect.

Towards a unified description of the hydrogen bond network of liquid water: A dynamics based approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozkanlar, Abdullah, E-mail: abdullah.ozkanlar@wsu.edu; Zhou, Tiecheng; Clark, Aurora E., E-mail: auclark@wsu.edu

2014-12-07

The definition of a hydrogen bond (H-bond) is intimately related to the topological and dynamic properties of the hydrogen bond network within liquid water. The development of a universal H-bond definition for water is an active area of research as it would remove many ambiguities in the network properties that derive from the fixed definition employed to assign whether a water dimer is hydrogen bonded. This work investigates the impact that an electronic-structure based definition, an energetic, and a geometric definition of the H-bond has upon both topological and dynamic network behavior of simulated water. In each definition, the usemore » of a cutoff (either geometric or energetic) to assign the presence of a H-bond leads to the formation of transiently bonded or broken dimers, which have been quantified within the simulation data. The relative concentration of transient species, and their duration, results in two of the three definitions sharing similarities in either topological or dynamic features (H-bond distribution, H-bond lifetime, etc.), however no two definitions exhibit similar behavior for both classes of network properties. In fact, two networks with similar local network topology (as indicated by similar average H-bonds) can have dramatically different global network topology (as indicated by the defect state distributions) and altered H-bond lifetimes. A dynamics based correction scheme is then used to remove artificially transient H-bonds and to repair artificially broken bonds within the network such that the corrected network exhibits the same structural and dynamic properties for two H-bond definitions (the properties of the third definition being significantly improved). The algorithm described represents a significant step forward in the development of a unified hydrogen bond network whose properties are independent of the original hydrogen bond definition that is employed.« less

DFT studies of the vibrational spectra of salicylic acid and related compounds

USDA-ARS?s Scientific Manuscript database

Compounds that exhibit intra- and intermolecular hydrogen bonds can have infrared and Raman spectra that show evidences of these hydrogen bonds. In modeling the vibrational spectra of such compounds, the addition of explicit hydrogen bonding species (e.g. solvent molecules) can often improve agreeme...

Hydrogen bonding directed self-assembly of small-molecule amphiphiles in water.

PubMed

Xu, Jiang-Fei; Niu, Li-Ya; Chen, Yu-Zhe; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

2014-08-01

Compounds comprising one or two quadruply hydrogen bonding units, 2-ureido-4[1H]-pyrimidinone (UPy) and tris(tetraethylene glycol monomethyl ether) moieties, were reported to form highly stable hydrogen-bonded assemblies in water. Compound 1, containing one UPy, assembles into vesicles, and compound 2, containing two UPy units, forms micelles. The aggregates disassemble reversibly when the solution pH is raised to 9.0 or above. The results demonstrate the utility of hydrogen bonding to direct the self-assembly of small-molecule building blocks in aqueous media.

Estimation of the degree of hydrogen bonding between quinoline and water by ultraviolet-visible absorbance spectroscopy in sub- and supercritical water

NASA Astrophysics Data System (ADS)

Osada, Mitsumasa; Toyoshima, Katsunori; Mizutani, Takakazu; Minami, Kimitaka; Watanabe, Masaru; Adschiri, Tadafumi; Arai, Kunio

2003-03-01

UV-visible spectra of quinoline was measured in sub- and supercritical water (25 °C

On the cooperativity of association and reference energy scales in thermodynamic perturbation theory

NASA Astrophysics Data System (ADS)

Marshall, Bennett D.

2016-11-01

Equations of state for hydrogen bonding fluids are typically described by two energy scales. A short range highly directional hydrogen bonding energy scale as well as a reference energy scale which accounts for dispersion and orientationally averaged multi-pole attractions. These energy scales are always treated independently. In recent years, extensive first principles quantum mechanics calculations on small water clusters have shown that both hydrogen bond and reference energy scales depend on the number of incident hydrogen bonds of the water molecule. In this work, we propose a new methodology to couple the reference energy scale to the degree of hydrogen bonding in the fluid. We demonstrate the utility of the new approach by showing that it gives improved predictions of water-hydrocarbon mutual solubilities.

Hirshfeld atom refinement for modelling strong hydrogen bonds.

PubMed

Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

2014-09-01

High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

Can Csbnd H⋯Fsbnd C hydrogen bonds alter crystal packing features in the presence of Nsbnd H⋯Odbnd C hydrogen bond?

NASA Astrophysics Data System (ADS)

Yadav, Hare Ram; Choudhury, Angshuman Roy

2017-12-01

Intermolecular interactions involving organic fluorine have been the contemporary field of research in the area of organic solid state chemistry. While a group of researchers had refuted the importance of "organic fluorine" in guiding crystal structures, others have provided evidences for in favor of fluorine mediated interactions in the solid state. Many systematic studies have indicated that the "organic fluorine" is capable of offering weak hydrogen bonds through various supramolecular synthons, mostly in the absence of other stronger hydrogen bonds. Analysis of fluorine mediated interaction in the presence of strong hydrogen bonds has not been highlighted in detail. Hence a thorough structural investigation is needed to understand the role of "organic fluorine" in crystal engineering of small organic fluorinated molecules having the possibility of strong hydrogen bond formation in the solution and in the solid state. To fulfil this aim, we have synthesized a series of fluorinated amides using 3-methoxyphenylacetic acid and fluorinated anilines and studied their structural properties through single crystal and powder X-ray diffraction methods. Our results indicated that the "organic fluorine" plays a significant role in altering the packing characteristics of the molecule in building specific crystal lattices even in the presence of strong hydrogen bond.

Pyrrolic tripodal receptors for carbohydrates. Role of functional groups and binding geometry on carbohydrate recognition.

PubMed

Cacciarini, Martina; Nativi, Cristina; Norcini, Martina; Staderini, Samuele; Francesconi, Oscar; Roelens, Stefano

2011-02-21

The contribution from several H-bonding groups and the impact of geometric requirements on the binding ability of benzene-based tripodal receptors toward carbohydrates have been investigated by measuring the affinity of a set of structures toward octyl β-D-glucopyranoside, selected as a representative monosaccharide. The results reported in the present study demonstrate that a judicious choice of correct geometry and appropriate functional groups is critical to achieve the complementary hydrogen bonding interactions required for an effective carbohydrate recognition.

Conformation-induced remote meta-C-H activation of amines

NASA Astrophysics Data System (ADS)

Tang, Ri-Yuan; Li, Gang; Yu, Jin-Quan

2014-03-01

Achieving site selectivity in carbon-hydrogen (C-H) functionalization reactions is a long-standing challenge in organic chemistry. The small differences in intrinsic reactivity of C-H bonds in any given organic molecule can lead to the activation of undesired C-H bonds by a non-selective catalyst. One solution to this problem is to distinguish C-H bonds on the basis of their location in the molecule relative to a specific functional group. In this context, the activation of C-H bonds five or six bonds away from a functional group by cyclometallation has been extensively studied. However, the directed activation of C-H bonds that are distal to (more than six bonds away) functional groups has remained challenging, especially when the target C-H bond is geometrically inaccessible to directed metallation owing to the ring strain encountered in cyclometallation. Here we report a recyclable template that directs the olefination and acetoxylation of distal meta-C-H bonds--as far as 11 bonds away--of anilines and benzylic amines. This template is able to direct the meta-selective C-H functionalization of bicyclic heterocycles via a highly strained, tricyclic-cyclophane-like palladated intermediate. X-ray and nuclear magnetic resonance studies reveal that the conformational biases induced by a single fluorine substitution in the template can be enhanced by using a ligand to switch from ortho- to meta-selectivity.

Conformation-induced remote meta-C-H activation of amines.

PubMed

Tang, Ri-Yuan; Li, Gang; Yu, Jin-Quan

2014-03-13

Achieving site selectivity in carbon-hydrogen (C-H) functionalization reactions is a long-standing challenge in organic chemistry. The small differences in intrinsic reactivity of C-H bonds in any given organic molecule can lead to the activation of undesired C-H bonds by a non-selective catalyst. One solution to this problem is to distinguish C-H bonds on the basis of their location in the molecule relative to a specific functional group. In this context, the activation of C-H bonds five or six bonds away from a functional group by cyclometallation has been extensively studied. However, the directed activation of C-H bonds that are distal to (more than six bonds away) functional groups has remained challenging, especially when the target C-H bond is geometrically inaccessible to directed metallation owing to the ring strain encountered in cyclometallation. Here we report a recyclable template that directs the olefination and acetoxylation of distal meta-C-H bonds--as far as 11 bonds away--of anilines and benzylic amines. This template is able to direct the meta-selective C-H functionalization of bicyclic heterocycles via a highly strained, tricyclic-cyclophane-like palladated intermediate. X-ray and nuclear magnetic resonance studies reveal that the conformational biases induced by a single fluorine substitution in the template can be enhanced by using a ligand to switch from ortho- to meta-selectivity.

A DFT and ab initio benchmarking study of metal-alkane interactions and the activation of carbon-hydrogen bonds.

PubMed

Flener-Lovitt, Charity; Woon, David E; Dunning, Thom H; Girolami, Gregory S

2010-02-04

Density functional theory and ab initio methods have been used to calculate the structures and energies of minima and transition states for the reactions of methane coordinated to a transition metal. The reactions studied are reversible C-H bond activation of the coordinated methane ligand to form a transition metal methyl hydride complex and dissociation of the coordinated methane ligand. The reaction sequence can be summarized as L(x)M(CH(3))H <==> L(x)M(CH(4)) <==> L(x)M + CH(4), where L(x)M is the osmium-containing fragment (C(5)H(5))Os(R(2)PCH(2)PR(2))(+) and R is H or CH(3). Three-center metal-carbon-hydrogen interactions play an important role in this system. Both basis sets and functionals have been benchmarked in this work, including new correlation consistent basis sets for a third transition series element, osmium. Double zeta quality correlation consistent basis sets yield energies close to those from calculations with quadruple-zeta basis sets, with variations that are smaller than the differences between functionals. The energies of important species on the potential energy surface, calculated by using 10 DFT functionals, are compared both to experimental values and to CCSD(T) single point calculations. Kohn-Sham natural bond orbital descriptions are used to understand the differences between functionals. Older functionals favor electrostatic interactions over weak donor-acceptor interactions and, therefore, are not particularly well suited for describing systems--such as sigma-complexes--in which the latter are dominant. Newer kinetic and dispersion-corrected functionals such as MPW1K and M05-2X provide significantly better descriptions of the bonding interactions, as judged by their ability to predict energies closer to CCSD(T) values. Kohn-Sham and natural bond orbitals are used to differentiate between bonding descriptions. Our evaluations of these basis sets and DFT functionals lead us to recommend the use of dispersion corrected functionals in conjunction with double-zeta or larger basis sets with polarization functions for calculations involving weak interactions, such as those found in sigma-complexes with transition metals.

Electronegativity estimator built on QTAIM-based domains of the bond electron density.

PubMed

Ferro-Costas, David; Pérez-Juste, Ignacio; Mosquera, Ricardo A

2014-05-15

The electron localization function, natural localized molecular orbitals, and the quantum theory of atoms in molecules have been used all together to analyze the bond electron density (BED) distribution of different hydrogen-containing compounds through the definition of atomic contributions to the bonding regions. A function, gAH , obtained from those contributions is analyzed along the second and third periods of the periodic table. It exhibits periodic trends typically assigned to the electronegativity (χ), and it is also sensitive to hybridization variations. This function also shows an interesting S shape with different χ-scales, Allred-Rochow's being the one exhibiting the best monotonical increase with regard to the BED taken by each atom of the bond. Therefore, we think this χ can be actually related to the BED distribution. Copyright © 2014 Wiley Periodicals, Inc.

Activation of carbon-hydrogen bonds via 1,2-addition across M-X (X = OH or NH(2)) bonds of d(6) transition metals as a potential key step in hydrocarbon functionalization: a computational study.

PubMed

Cundari, Thomas R; Grimes, Thomas V; Gunnoe, T Brent

2007-10-31

Recent reports of 1,2-addition of C-H bonds across Ru-X (X = amido, hydroxo) bonds of TpRu(PMe3)X fragments {Tp = hydridotris(pyrazolyl)borate} suggest opportunities for the development of new catalytic cycles for hydrocarbon functionalization. In order to enhance understanding of these transformations, computational examinations of the efficacy of model d6 transition metal complexes of the form [(Tab)M(PH3)2X]q (Tab = tris-azo-borate; X = OH, NH2; q = -1 to +2; M = TcI, Re(I), Ru(II), Co(III), Ir(III), Ni(IV), Pt(IV)) for the activation of benzene C-H bonds, as well as the potential for their incorporation into catalytic functionalization cycles, are presented. For the benzene C-H activation reaction steps, kite-shaped transition states were located and found to have relatively little metal-hydrogen interaction. The C-H activation process is best described as a metal-mediated proton transfer in which the metal center and ligand X function as an activating electrophile and intramolecular base, respectively. While the metal plays a primary role in controlling the kinetics and thermodynamics of the reaction coordinate for C-H activation/functionalization, the ligand X also influences the energetics. On the basis of three thermodynamic criteria characterizing salient energetic aspects of the proposed catalytic cycle and the detailed computational studies reported herein, late transition metal complexes (e.g., Pt, Co, etc.) in the d6 electron configuration {especially the TabCo(PH3)2(OH)+ complex and related Co(III) systems} are predicted to be the most promising for further catalyst investigation.

Liquid crystal nanocomposites produced by mixtures of hydrogen bonded achiral liquid crystals and functionalized carbon nanotubes

NASA Astrophysics Data System (ADS)

Katranchev, B.; Petrov, M.; Keskinova, E.; Naradikian, H.; Rafailov, P. M.; Dettlaff-Weglikowska, U.; Spassov, T.

2014-12-01

The liquid crystalline (LC) nature of alkyloxybenzoic acids is preserved after adding of any mesogenic or non-mesogenic compound through hydrogen bonding. However, this noncovalent interaction provokes a sizable effect on the physical properties as, e. g. melting point and mesomorphic states. In the present work we investigate nanocomposites, prepared by mixture of the eighth homologue of p-n-alkyloxybenzoic acids (8OBA) with single-walled carbon nanotubes (SWCNT) with the purpose to modify the optical properties of the liquid crystal. We exercise optical control on the LC system by inserting SWCNT specially functionalized by carboxylic groups. Since the liquid crystalline state combines order and mobility at the molecular (nanoscale) level, molecular modification can lead to different macroscopical nanocomposite symmetry. The thermal properties of the functionalized nanocomposite are confirmed by DSC analyses. The mechanism of the interaction between surface-treated nanoparticles (functionalized nanotubes) and the liquid crystal 8OBA bent- dimer molecules is briefly discussed.

Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins.

PubMed

Deb, Pranab; Haldar, Tapas; Kashid, Somnath M; Banerjee, Subhrashis; Chakrabarty, Suman; Bagchi, Sayan

2016-05-05

Noncovalent interactions, in particular the hydrogen bonds and nonspecific long-range electrostatic interactions are fundamental to biomolecular functions. A molecular understanding of the local electrostatic environment, consistently for both specific (hydrogen-bonding) and nonspecific electrostatic (local polarity) interactions, is essential for a detailed understanding of these processes. Vibrational Stark Effect (VSE) has proven to be an extremely useful method to measure the local electric field using infrared spectroscopy of carbonyl and nitrile based probes. The nitrile chemical group would be an ideal choice because of its absorption in an infrared spectral window transparent to biomolecules, ease of site-specific incorporation into proteins, and common occurrence as a substituent in various drug molecules. However, the inability of VSE to describe the dependence of IR frequency on electric field for hydrogen-bonded nitriles to date has severely limited nitrile's utility to probe the noncovalent interactions. In this work, using infrared spectroscopy and atomistic molecular dynamics simulations, we have reported for the first time a linear correlation between nitrile frequencies and electric fields in a wide range of hydrogen-bonding environments that may bridge the existing gap between VSE and H-bonding interactions. We have demonstrated the robustness of this field-frequency correlation for both aromatic nitriles and sulfur-based nitriles in a wide range of molecules of varying size and compactness, including small molecules in complex solvation environments, an amino acid, disordered peptides, and structured proteins. This correlation, when coupled to VSE, can be used to quantify noncovalent interactions, specific or nonspecific, in a consistent manner.

Structural characterization of 1,3-propanedithiols that feature carboxylic acids: Homologues of mercury chelating agents ✩

PubMed Central

Sattler, Wesley; Palmer, Joshua H.; Bridges, Christy C.; Joshee, Lucy; Zalups, Rudolfs K.; Parkin, Gerard

2013-01-01

The molecular structures of a series of 1,3-propanedithiols that contain carboxylic acid groups, namely rac- and meso-2,4-dimercaptoglutaric acid (H4DMGA) and 2-carboxy-1,3-propanedithiol (H3DMCP), have been determined by X-ray diffraction. Each compound exhibits two centrosymmetric intermolecular hydrogen bonding interactions between pairs of carboxylic acid groups, which result in a dimeric structure for H3DMCP and a polymeric tape-like structure for rac- and meso-H4DMGA. Significantly, the hydrogen bonding motifs observed for rac- and meso-H4DMGA are very different to those observed for the 1,2-dithiol, rac-2,3-dimercaptosuccinic acid (rac-H4DMSA), in which the two oxygen atoms of each carboxylic acid group hydrogen bond to two different carboxylic acid groups, thereby resulting in a hydrogen bonded sheet-like structure rather than a tape. Density functional theory calculations indicate that 1,3-dithiolate coordination to mercury results in larger S–Hg–S bond angles than does 1,2-dithiolate coordination, but these angles are far from linear. As such, κ2-S2 coordination of these dithiolate ligands is expected to be associated with mercury coordination numbers of greater than two. In vivo studies demonstrate that both rac-H4DMGA and H3DMCP reduce the renal burden of mercury in rats, although the compounds are not as effective as either 2,3-dimercaptopropane-1-sulfonic acid (H3DMPS) or meso-H4DMSA. PMID:24187425

Theoretical study of the changes in the vibrational characteristics arising from the hydrogen bonding between Vitamin C ( L-ascorbic acid) and H 2O

NASA Astrophysics Data System (ADS)

Dimitrova, Yordanka

2006-02-01

The vibrational characteristics (vibrational frequencies, infrared intensities and Raman activities) for the hydrogen-bonded system of Vitamin C ( L-ascorbic acid) with five water molecules have been predicted using ab initio SCF/6-31G(d, p) calculations and DFT (BLYP) calculations with 6-31G(d, p) and 6-31++G(d, p) basis sets. The changes in the vibrational characteristics from free monomers to a complex have been calculated. The ab initio and BLYP calculations show that the complexation between Vitamin C and five water molecules leads to large red shifts of the stretching vibrations for the monomer bonds involved in the hydrogen bonding and very strong increase in their IR intensity. The predicted frequency shifts for the stretching vibrations from Vitamin C taking part in the hydrogen bonding are up to -508 cm -1. The magnitude of the wavenumber shifts is indicative of relatively strong OH···H hydrogen-bonded interactions. In the same time the IR intensity and Raman activity of these vibrations increase upon complexation. The IR intensity increases dramatically (up to 12 times) and Raman activity increases up to three times. The ab initio and BLYP calculations show, that the symmetric OH vibrations of water molecules are more sensitive to the complexation. The hydrogen bonding leads to very large red shifts of these vibrations and very strong increase in their IR intensity. The asymmetric OH stretching vibrations of water, free from hydrogen bonding are less sensitive to the complexation than the hydrogen-bonded symmetric O sbnd H stretching vibrations. The increases of the IR intensities for these vibrations are lower and red shifts are negligible.

Computational study of red- and blue-shifted Csbnd H⋯Se hydrogen bond in Q3Csbnd H⋯SeH2 (Q = Cl, F, H) complexes

NASA Astrophysics Data System (ADS)

Chopra, Pragya; Chakraborty, Shamik

2018-01-01

This work presents Csbnd H⋯Se hydrogen bonding interaction at the MP2 level of theory. The system Q3Csbnd H⋯SeH2 (Q = Cl, F, and H) provides an opportunity to investigate red- and blue-shifted hydrogen bonds. The origin of the red- and blue-shift in Csbnd H stretching frequency has been investigated using Natural Bond Orbital analysis. A large amount of electron density is being transferred to the σ∗Csbnd H orbital in red-shifted Cl3Csbnd H⋯SeH2. Electron density transfer in the blue-shifted F3Csbnd H⋯SeH2 is primarily to the remote fluorine atoms. Further, due to polarization of the Csbnd H bond, the contradicting effects of rehybridization and hyperconjugation are important. The extent of hyperconjugation reigns predominant in explaining the nature of the Csbnd H⋯Se hydrogen bond in Q3Csbnd H⋯SeH2 complexes as the hydrogen bond acceptor remain same in this investigation. Red- and blue-shift in Q3Csbnd H⋯SeH2 (Q = Cl and F) complexes is best described by pro-improper hydrogen bond donor concept.

Significant Quantum Effects in Hydrogen Activation

DOE PAGES

Kyriakou, Georgios; Davidson, Erlend R. M.; Peng, Guowen; ...

2014-03-31

Dissociation of molecular hydrogen is an important step in a wide variety of chemical, biological, and physical processes. Due to the light mass of hydrogen, it is recognized that quantum effects are often important to its reactivity. However, understanding how quantum effects impact the reactivity of hydrogen is still in its infancy. Here, we examine this issue using a well-defined Pd/Cu(111) alloy that allows the activation of hydrogen and deuterium molecules to be examined at individual Pd atom surface sites over a wide range of temperatures. Experiments comparing the uptake of hydrogen and deuterium as a function of temperature revealmore » completely different behavior of the two species. The rate of hydrogen activation increases at lower sample temperature, whereas deuterium activation slows as the temperature is lowered. Density functional theory simulations in which quantum nuclear effects are accounted for reveal that tunneling through the dissociation barrier is prevalent for H 2 up to ~190 K and for D 2 up to ~140 K. Kinetic Monte Carlo simulations indicate that the effective barrier to H 2 dissociation is so low that hydrogen uptake on the surface is limited merely by thermodynamics, whereas the D 2 dissociation process is controlled by kinetics. These data illustrate the complexity and inherent quantum nature of this ubiquitous and seemingly simple chemical process. Here, examining these effects in other systems with a similar range of approaches may uncover temperature regimes where quantum effects can be harnessed, yielding greater control of bond-breaking processes at surfaces and uncovering useful chemistries such as selective bond activation or isotope separation.« less

Metal-functionalized silicene for efficient hydrogen storage.

PubMed

Hussain, Tanveer; Chakraborty, Sudip; Ahuja, Rajeev

2013-10-21

First-principles calculations based on density functional theory are used to investigate the electronic structure along with the stability, bonding mechanism, band gap, and charge transfer of metal-functionalized silicene to envisage its hydrogen-storage capacity. Various metal atoms including Li, Na, K, Be, Mg, and Ca are doped into the most stable configuration of silicene. The corresponding binding energies and charge-transfer mechanisms are discussed from the perspective of hydrogen-storage compatibility. The Li and Na metal dopants are found to be ideally suitable, not only for strong metal-to-substrate binding and uniform distribution over the substrate, but also for the high-capacity storage of hydrogen. The stabilities of both Li- and Na-functionalized silicene are also confirmed through molecular dynamics simulations. It is found that both of the alkali metals, Li(+) and Na(+), can adsorb five hydrogen molecules, attaining reasonably high storage capacities of 7.75 and 6.9 wt %, respectively, with average adsorption energies within the range suitable for practical hydrogen-storage applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds

PubMed Central

Potapova, Olga; Chan, Chikio; DeLucia, Angela M.; Helquist, Sandra A.; Kool, Eric T.; Grindley, Nigel D. F.; Joyce, Catherine M.

2008-01-01

We report the first pre-steady-state kinetic studies of DNA replication in the absence of hydrogen bonds. We have used nonpolar nucleotide analogues that mimic the shape of a Watson-Crick base pair in order to investigate the kinetic consequences of a lack of hydrogen bonds in the polymerase reaction catalyzed by the Klenow fragment of DNA Polymerase I from Escherichia coli. With a thymine isostere lacking hydrogen bonding ability in the nascent pair, the efficiency (kpol/Kd) of the polymerase reaction is decreased by 30-fold, affecting ground state (Kd) and transition state (kpol) approximately equally. When both thymine and adenine analogues in the nascent pair lack hydrogen bonding ability, the efficiency of the polymerase reaction is decreased by about 1000-fold, with most the decrease attributable to the transition state. Reactions using nonpolar analogues at the primer terminal base pair demonstrated the requirement for a hydrogen bond between the polymerase and the minor groove of the primer-terminal base. The R668A mutation of Klenow fragment abolished this requirement, identifying R668 as the probable hydrogen bond donor. Detailed examination of the kinetic data suggested that Klenow fragment has an extremely low tolerance of even minor deviations of the analogue base pairs from ideal Watson-Crick geometry. Consistent with this idea, some analogue pairings were better tolerated by Klenow fragment mutants having more spacious active sites. By contrast, the Y-family polymerase Dbh was much less sensitive to changes in base pair dimensions, and more dependent on hydrogen bonding between base-paired partners. PMID:16411765

Elucidation of metal-ion accumulation induced by hydrogen bonds on protein surfaces by using porous lysozyme crystals containing Rh(III) ions as the model surfaces.

PubMed

Ueno, Takafumi; Abe, Satoshi; Koshiyama, Tomomi; Ohki, Takahiro; Hikage, Tatsuo; Watanabe, Yoshihito

2010-03-01

Metal-ion accumulation on protein surfaces is a crucial step in the initiation of small-metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh(III) ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino-acid residues to capture Rh(III) ions. ii) Water molecules pre-organized by hydrogen bonds can stabilize Rh(III) coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino-acid residues can be replaced by Rh(III) ions to form polynuclear structures with the residues. iv) Rh(III) aqua complexes are retained on amino-acid residues through stabilizing hydrogen bonds even at low pH (approximately 2). These metal-protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.

Hydrogen bonds between the alpha and beta subunits of the F1-ATPase allow communication between the catalytic site and the interface of the beta catch loop and the gamma subunit.

PubMed

Boltz, Kathryn W; Frasch, Wayne D

2006-09-19

F(1)-ATPase mutations in Escherichia coli that changed the strength of hydrogen bonds between the alpha and beta subunits in a location that links the catalytic site to the interface between the beta catch loop and the gamma subunit were examined. Loss of the ability to form the hydrogen bonds involving alphaS337, betaD301, and alphaD335 lowered the k(cat) of ATPase and decreased its susceptibility to Mg(2+)-ADP-AlF(n) inhibition, while mutations that maintain or strengthen these bonds increased the susceptibility to Mg(2+)-ADP-AlF(n) inhibition and lowered the k(cat) of ATPase. These data suggest that hydrogen bonds connecting alphaS337 to betaD301 and betaR323 and connecting alphaD335 to alphaS337 are important to transition state stabilization and catalytic function that may result from the proper alignment of catalytic site residues betaR182 and alphaR376 through the VISIT sequence (alpha344-348). Mutations betaD301E, betaR323K, and alphaR282Q changed the rate-limiting step of the reaction as determined by an isokinetic plot. Hydrophobic mutations of betaR323 decreased the susceptibility to Mg(2+)-ADP-AlF(n)() inhibition and lowered the number of interactions required in the rate-limiting step yet did not affect the k(cat) of ATPase, suggesting that betaR323 is important to transition state formation. The decreased rate of ATP synthase-dependent growth and decreased level of lactate-dependent quenching observed with alphaD335, betaD301, and alphaE283 mutations suggest that these residues may be important to the formation of an alternative set of hydrogen bonds at the interface of the alpha and beta subunits that permits the release of intersubunit bonds upon the binding of ATP, allowing gamma rotation in the escapement mechanism.

Uniform Atomic Layer Deposition of Al2O3 on Graphene by Reversible Hydrogen Plasma Functionalization

PubMed Central

2017-01-01

A novel method to form ultrathin, uniform Al2O3 layers on graphene using reversible hydrogen plasma functionalization followed by atomic layer deposition (ALD) is presented. ALD on pristine graphene is known to be a challenge due to the absence of dangling bonds, leading to nonuniform film coverage. We show that hydrogen plasma functionalization of graphene leads to uniform ALD of closed Al2O3 films down to 8 nm in thickness. Hall measurements and Raman spectroscopy reveal that the hydrogen plasma functionalization is reversible upon Al2O3 ALD and subsequent annealing at 400 °C and in this way does not deteriorate the graphene’s charge carrier mobility. This is in contrast with oxygen plasma functionalization, which can lead to a uniform 5 nm thick closed film, but which is not reversible and leads to a reduction of the charge carrier mobility. Density functional theory (DFT) calculations attribute the uniform growth on both H2 and O2 plasma functionalized graphene to the enhanced adsorption of trimethylaluminum (TMA) on these surfaces. A DFT analysis of the possible reaction pathways for TMA precursor adsorption on hydrogenated graphene predicts a binding mechanism that cleans off the hydrogen functionalities from the surface, which explains the observed reversibility of the hydrogen plasma functionalization upon Al2O3 ALD. PMID:28405059

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of p-amino acetanilide.

PubMed

Abraham, Jose P; Sajan, D; Joe, I Hubert; Jayakumar, V S

2008-11-15

The infrared absorption, Raman spectra and SERS spectra of p-amino acetanilide have been analyzed with the aid of density functional theory calculations at B3LYP/6-311G(d,p) level. The electric dipole moment (mu) and the first hyperpolarizability (beta) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the synthesized molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Computed geometries reveal that the PAA molecule is planar, while secondary amide group is twisted with respect to the phenyl ring is found, upon hydrogen bonding. The hyperconjugation of the C=O group with adjacent C-C bond and donor-acceptor interaction associated with the secondary amide have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation and hyperconjugation. The existence of intramolecular C=O...H hydrogen bonded have been investigated by means of the natural bonding orbital (NBO) analysis. The influence of the decrease of N-H and C=O bond orders and increase of C-N bond orders due to donor-acceptor interaction has been identified in the vibrational spectra. The SERS spectral analysis reveals that the large enhancement of in-plane bending, out of plane bending and ring breathing modes in the surface-enhanced Raman scattering spectrum indicates that the molecule is adsorbed on the silver surface in a 'atleast vertical' configuration, with the ring perpendicular to the silver surface.

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of p-amino acetanilide

NASA Astrophysics Data System (ADS)

Abraham, Jose P.; Sajan, D.; Joe, I. Hubert; Jayakumar, V. S.

2008-11-01

The infrared absorption, Raman spectra and SERS spectra of p-amino acetanilide have been analyzed with the aid of density functional theory calculations at B3LYP/6-311G(d,p) level. The electric dipole moment ( μ) and the first hyperpolarizability ( β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the synthesized molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Computed geometries reveal that the PAA molecule is planar, while secondary amide group is twisted with respect to the phenyl ring is found, upon hydrogen bonding. The hyperconjugation of the C dbnd O group with adjacent C-C bond and donor-acceptor interaction associated with the secondary amide have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation and hyperconjugation. The existence of intramolecular C dbnd O⋯H hydrogen bonded have been investigated by means of the natural bonding orbital (NBO) analysis. The influence of the decrease of N-H and C dbnd O bond orders and increase of C-N bond orders due to donor-acceptor interaction has been identified in the vibrational spectra. The SERS spectral analysis reveals that the large enhancement of in-plane bending, out of plane bending and ring breathing modes in the surface-enhanced Raman scattering spectrum indicates that the molecule is adsorbed on the silver surface in a 'atleast vertical' configuration, with the ring perpendicular to the silver surface.

A complete active space valence bond method with nonorthogonal orbitals

NASA Astrophysics Data System (ADS)

Hirao, Kimihiko; Nakano, Haruyuki; Nakayama, Kenichi

1997-12-01

A complete active space self-consistent field (SCF) wave function is transformed into a valence bond type representation built from nonorthogonal orbitals, each strongly localized on a single atom. Nonorthogonal complete active space SCF orbitals are constructed by Ruedenberg's projected localization procedure so that they have maximal overlaps with the corresponding minimum basis set of atomic orbitals of the free-atoms. The valence bond structures which are composed of such nonorthogonal quasiatomic orbitals constitute the wave function closest to the concept of the oldest and most simple valence bond method. The method is applied to benzene, butadiene, hydrogen, and methane molecules and compared to the previously proposed complete active space valence bond approach with orthogonal orbitals. The results demonstrate the validity of the method as a powerful tool for describing the electronic structure of various molecules.

2-Amino-5-chloro-pyrimidin-1-ium hydrogen maleate.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Rajakannan, Venkatachalam

2012-01-01

In the title salt, C(4)H(5)ClN(3) (+)·C(4)H(3)O(4) (-), the 2-amino-5-chloro-pyrimidinium cation is protonated at one of its pyrimidine N atoms. In the roughly planar (r.m.s. deviation = 0.026 Å) hydrogen malate anion, an intra-molecular O-H⋯O hydrogen bond generates an S(7) ring. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl-ate O atoms of the anion via a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. The ion pairs are connected via further N-H⋯O hydrogen bonds and a short C-H⋯O inter-action, forming layers lying parallel to the bc plane.

Towards mild metal-catalyzed C-H bond activation.

PubMed

Wencel-Delord, Joanna; Dröge, Thomas; Liu, Fan; Glorius, Frank

2011-09-01

Functionalizing traditionally inert carbon-hydrogen bonds represents a powerful transformation in organic synthesis, providing new entries to valuable structural motifs and improving the overall synthetic efficiency. C-H bond activation, however, often necessitates harsh reaction conditions that result in functional group incompatibilities and limited substrate scope. An understanding of the reaction mechanism and rational design of experimental conditions have led to significant improvement in both selectivity and applicability. This critical review summarizes and discusses endeavours towards the development of mild C-H activation methods and wishes to trigger more research towards this goal. In addition, we examine select examples in complex natural product synthesis to demonstrate the synthetic utility of mild C-H functionalization (84 references). This journal is © The Royal Society of Chemistry 2011

4-Mercaptophenylboronic acid: conformation, FT-IR, Raman, OH stretching and theoretical studies.

PubMed

Parlak, Cemal; Ramasami, Ponnadurai; Tursun, Mahir; Rhyman, Lydia; Kaya, Mehmet Fatih; Atar, Necip; Alver, Özgür; Şenyel, Mustafa

2015-06-05

4-Mercaptophenylboronic acid (4-mpba, C6H7BO2S) was investigated experimentally by vibrational spectroscopy. The molecular structure and spectroscopic parameters were studied by computational methods. The molecular dimer was investigated for intermolecular hydrogen bonding. Potential energy distribution analysis of normal modes was performed to identify characteristic frequencies. The present work provides a simple physical picture of the OH stretch vibrational spectra of 4-mpba and analogues of the compound studied. When the different computational methods are compared, there is a strong evidence of the better performance of the BLYP functional than the popular B3LYP functional to describe hydrogen bonding in the dimer. The findings of this research work should be useful to experimentalists in their quests for functionalised 4-mpba derivatives. Copyright © 2015 Elsevier B.V. All rights reserved.

Tuning the nature and stability of self-assemblies formed by ester benzene 1,3,5-tricarboxamides: the crucial role played by the substituents.

PubMed

Desmarchelier, Alaric; Alvarenga, Bruno Giordano; Caumes, Xavier; Dubreucq, Ludovic; Troufflard, Claire; Tessier, Martine; Vanthuyne, Nicolas; Idé, Julien; Maistriaux, Thomas; Beljonne, David; Brocorens, Patrick; Lazzaroni, Roberto; Raynal, Matthieu; Bouteiller, Laurent

2016-09-20

As the benzene 1,3,5-tricarboxamide (BTA) moiety is commonly used as the central assembling unit for the construction of functionalized supramolecular architectures, strategies to tailor the nature and stability of BTA assemblies are needed. The assembly properties of a library of structurally simple BTAs derived from amino dodecyl esters (ester BTAs, 13 members) have been studied, either in the bulk or in cyclohexane solutions, by means of a series of analytical methods (NMR, DSC, POM, FT-IR, UV-Vis, CD, ITC, high-sensitivity DSC, SANS). Two types of hydrogen-bonded species have been identified and characterized: the expected amide-bonded helical rods (or stacks) that are structurally similar to those formed by BTAs with simple alkyl side chains (alkyl BTAs), and ester-bonded dimers in which the BTAs are connected by means of hydrogen bonds linking the amide N-H and the ester C[double bond, length as m-dash]O. MM/MD calculations coupled with simulations of CD spectra allow for the precise determination of the molecular arrangement and of the hydrogen bond pattern of these dimers. Our study points out the crucial influence of the substituent attached on the amino-ester α-carbon on the relative stability of the rod-like versus dimeric assemblies. By varying this substituent, one can precisely tune the nature of the dominant hydrogen-bonded species (stacks or dimers) in the neat compounds and in cyclohexane over a wide range of temperatures and concentrations. In the neat BTAs, stacks are stable up to 213 °C and dimers above 180 °C whilst in cyclohexane stacks form at c* > 3 × 10 -5 M at 20 °C and dimers are stable up to 80 °C at 7 × 10 -6 M. Ester BTAs that assemble into stacks form a liquid-crystalline phase and yield gels or viscous solutions in cyclohexane, demonstrating the importance of controlling the structure of these assemblies. Our systematic study of these structurally similar ester BTAs also allows for a better understanding of how a single atom or moiety can impact the nature and stability of BTA aggregates, which is of importance for the future development of functionalized BTA supramolecular polymers.

Characterization of the hydrogen-bond network of water around sucrose and trehalose: Microwave and terahertz spectroscopic study

NASA Astrophysics Data System (ADS)

Shiraga, Keiichiro; Adachi, Aya; Nakamura, Masahito; Tajima, Takuro; Ajito, Katsuhiro; Ogawa, Yuichi

2017-03-01

Modification of the water hydrogen bond network imposed by disaccharides is known to serve as a bioprotective agent in living organisms, though its comprehensive understanding is still yet to be reached. In this study, aiming to characterize the dynamical slowing down and destructuring effect of disaccharides, we performed broadband dielectric spectroscopy, ranging from 0.5 GHz to 12 THz, of sucrose and trehalose aqueous solutions. The destructuring effect was examined in two ways (the hydrogen bond fragmentation and disordering) and our result showed that both sucrose and trehalose exhibit an obvious destructuring effect with a similar strength, by fragmenting hydrogen bonds and distorting the tetrahedral-like structure of water. This observation strongly supports a chaotropic (structure-breaking) aspect of disaccharides on the water structure. At the same time, hydration water was found to exhibit slower dynamics and a greater reorientational cooperativity than bulk water because of the strengthened hydrogen bonds. These results lead to the conclusion that strong disaccharide-water hydrogen bonds structurally incompatible with native water-water bonds lead to the rigid but destructured hydrogen bond network around disaccharides. Another important finding in this study is that the greater dynamical slowing down of trehalose was found compared with that of sucrose, at variance with the destructuring effect where no solute dependent difference was observed. This discovery suggests that the exceptionally greater bioprotective impact especially of trehalose among disaccharides is mainly associated with the dynamical slowing down (rather than the destructuring effect).

Finite size effect on hydrogen bond cooperativity in (Ala)n polypeptides: A DFT study using numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Ireta, Joel; Scheffler, Matthias

2007-03-01

An accurate representation of the energetic contribution Ehb of hydrogen bonds to structure formation is paramount to understand the secondary structure stability of proteins, both qualitatively and quantitatively. However, Ehb depends strongly on its environment, and even on the surrounding peptide conformation itself. For instance, a short α-helical polypeptide (Ala)4 can not be stabilized by its single hydrogen bond, whereas an infinite α-helical chain (Ala)∞ is clearly energetically stable over a fully extended conformation. We here use all-electron density functional calculations in the PBE generalized gradient approximation by a recently developed, computationally efficient numeric atom-centered orbital based code^1 to investigate this H-bond cooperativity that is intrinsic to Alanine-based polypeptides (Ala)n (n=1-20,∞). We compare finite and infinite prototypical helical conformations (α, π, 310) on equal footing, with both neutral and ionic termination for finite (Ala)n peptides. Moderately sized NAO basis sets allow to capture Ehb with meV accuracy, revealing a clear jump in Ehb (cooperativity) when two H-bonds first appear in line, followed by slower and more continuous increase of Ehb towards n->∞. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide.

PubMed

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2013-09-01

In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm(-1)) and μ-Raman spectra (100-4000 cm(-1)) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the N-H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular N-H···S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented. Copyright © 2013 Elsevier B.V. All rights reserved.

Fabrication of sophisticated two-dimensional organic nanoarchitectures thought hydrogen bond mediated molecular self assembly

NASA Astrophysics Data System (ADS)

Silly, Fabien

2012-02-01

Complex supramolecular two-dimensional (2D) networks are attracting considerable interest as highly ordered functional materials for applications in nanotechnology. The challenge consists in tailoring the ordering of one or more molecular species into specific architectures over an extended length scale with molecular precision. Highly organized supramolecular arrays can be obtained through self-assembly of complementary molecules which can interlock via intermolecular interactions. Molecules forming hydrogen bonds (H-bonds) are especially interesting building blocks for creating sophisticated organic architectures due to high selectivity and directionality of these bindings. We used scanning tunnelling microscopy to investigate at the atomic scale the formation of H-bonded 2D organic nanoarchitectures on surfaces. We mixed perylene derivatives having rectangular shape with melamine and DNA base having triangular and non symmetric shape respectively. We observe that molecule substituents play a key role in formation of the multicomponent H-bonded architectures. We show that the 2D self-assembly of these molecules can be tailored by adjusting the temperature and molecular ratio. We used these stimuli to successfully create numerous close-packed and porous 2D multicomponent structures.

A second order thermodynamic perturbation theory for hydrogen bond cooperativity in water

NASA Astrophysics Data System (ADS)

Marshall, Bennett D.

2017-05-01

It has been extensively demonstrated through first principles quantum mechanics calculations that water exhibits strong hydrogen bond cooperativity. Equations of state developed from statistical mechanics typically assume pairwise additivity, meaning they cannot account for these 3-body and higher cooperative effects. In this paper, we extend a second order thermodynamic perturbation theory to correct for hydrogen bond cooperativity in 4 site water. We demonstrate that the theory predicts hydrogen bonding structure consistent spectroscopy, neutron diffraction, and molecular simulation data. Finally, we implement the approach into a general equation of state for water.

Methods of using ionic liquids having a fluoride anion as solvents

DOEpatents

Pagoria, Philip [Livermore, CA; Maiti, Amitesh [San Ramon, CA; Gash, Alexander [Brentwood, CA; Han, Thomas Yong [Pleasanton, CA; Orme, Christine [Oakland, CA; Fried, Laurence [Livermore, CA

2011-12-06

A method in one embodiment includes contacting a strongly hydrogen bonded organic material with an ionic liquid having a fluoride anion for solubilizing the strongly hydrogen bonded organic material; and maintaining the ionic liquid at a temperature of about 90.degree. C. or less during the contacting. A method in another embodiment includes contacting a strongly hydrogen bonded organic material with an ionic liquid having an acetate or formate anion for solubilizing the strongly hydrogen bonded organic material; and maintaining the ionic liquid at a temperature of less than about 90.degree. C. during the contacting.

Diethyl [(4-bromo­phen­yl)(5-chloro-2-hydroxy­anilino)meth­yl]phospho­nate

PubMed Central

Babu, V. H. H. Surendra; Krishnaiah, M.; Prasad, G. Syam; C. Suresh Reddy; Kant, Rajni

2009-01-01

In the title compound, C17H20BrClNO4P, inter­molecular C—H⋯O and N—H⋯O hydrogen bonds form centrosymmetric R 2 2(10) dimers linked through O—H⋯O inter­molecular hydrogen bonds, which form centrosymmetric R 2 2(16) dimers. All these hydrogen bonds form chains along [010]. In addition, the crystal structure is stabilized by weak C—H⋯Br hydrogen bonds. The very weak intramolecular N—H⋯O interaction forms a five-membered ring. PMID:21578446

Intramolecular Hydrogen Bond Activation: Thiourea-Organocatalyzed Enantioselective 1,3-Dipolar Cycloaddition of Salicylaldehyde-Derived Azomethine Ylides with Nitroalkenes.

PubMed

Esteban, Francisco; Cieślik, Wioleta; Arpa, Enrique M; Guerrero-Corella, Andrea; Díaz-Tendero, Sergio; Perles, Josefina; Fernández-Salas, José A; Fraile, Alberto; Alemán, José

2018-03-02

An organocatalytic strategy for the synthesis of tetrasubstituted pyrrolidines with monoactivated azomethine ylides in high enantiomeric excess and excellent exo/endo selectivity is presented. The key to success is the intramolecular activation via hydrogen bonding through an o -hydroxy group, which allows the dipolar cycloaddition to take place in the presence of azomethine ylides bearing only one activating group. The intramolecular hydrogen bond in the azomethine ylide and the intermolecular hydrogen bond with the catalyst have been demonstrated by DFT calculations and mechanistic proofs to be crucial for the reaction to proceed.

Evidence of quantum correlations in the H/D-transfer dynamics in the hydrogen bonds in partially deuterated benzoic acid crystals

NASA Astrophysics Data System (ADS)

Takeda, Sadamu; Tsuzumitani, Akihiko; Chatzidimitriou-Dreismann, C. A.

1992-10-01

A precise investigation of spin—lattice relaxation rates for protons and deuterons of partially deuterated benzoic acid crystals showed a remarkable quenching of the transfer rate of an HD pair in hydrogen-bonded dimeric units of carboxyl groups with increasing concentration of D in the surrounding hydrogen bonds. A similar effect was also observed for partially deuterated crystals of acetylenedicarboxylic acid. This finding supports recent theoretical predictions of thermally activated protonic quantum correlation in condensed matter and proposes a new mechanism for the proton transfer in hydrogen bonds in condensed matter.

Interrelationship among Fe-His Bond Strengths, Oxygen Affinities, and Intersubunit Hydrogen Bonding Changes upon Ligand Binding in the β Subunit of Human Hemoglobin: The Alkaline Bohr Effect.

PubMed

Nagatomo, Shigenori; Okumura, Miki; Saito, Kazuya; Ogura, Takashi; Kitagawa, Teizo; Nagai, Masako

2017-03-07

Regulation of the oxygen affinity of human adult hemoglobin (Hb A) at high pH, known as the alkaline Bohr effect, is essential for its physiological function. In this study, structural mechanisms of the alkaline Bohr effect and pH-dependent O 2 affinity changes were investigated via 1 H nuclear magnetic resonance and visible and UV resonance Raman spectra of mutant Hbs, Hb M Iwate (αH87Y) and Hb M Boston (αH58Y). It was found that even though the binding of O 2 to the α subunits is forbidden in the mutant Hbs, the O 2 affinity was higher at alkaline pH than at neutral pH, and concomitantly, the Fe-His stretching frequency of the β subunits was shifted to higher values. Thus, it was confirmed for the β subunits that the stronger the Fe-His bond, the higher the O 2 affinity. It was found in this study that the quaternary structure of α(Fe 3+ )β(Fe 2+ -CO) of the mutant Hb is closer to T than to the ordinary R at neutral pH. The retained Aspβ94-Hisβ146 hydrogen bond makes the extent of proton release smaller upon ligand binding from Hisβ146, known as one of residues contributing to the alkaline Bohr effect. For these T structures, the Aspα94-Trpβ37 hydrogen bond in the hinge region and the Tyrα42-Aspβ99 hydrogen bond in the switch region of the α 1 -β 2 interface are maintained but elongated at alkaline pH. Thus, a decrease in tension in the Fe-His bond of the β subunits at alkaline pH causes a substantial increase in the change in global structure upon binding of CO to the β subunit.

Vibrational dynamics of hydrogen-bonded complexes in solutions studied with ultrafast infrared pump-probe spectroscopy.

PubMed

Banno, Motohiro; Ohta, Kaoru; Yamaguchi, Sayuri; Hirai, Satori; Tominaga, Keisuke

2009-09-15

In aqueous solution, the basis of all living processes, hydrogen bonding exerts a powerful effect on chemical reactivity. The vibrational energy relaxation (VER) process in hydrogen-bonded complexes in solution is sensitive to the microscopic environment around the oscillator and to the geometrical configuration of the hydrogen-bonded complexes. In this Account, we describe the use of time-resolved infrared (IR) pump-probe spectroscopy to study the vibrational dynamics of (i) the carbonyl CO stretching modes in protic solvents and (ii) the OH stretching modes of phenol and carboxylic acid. In these cases, the carbonyl group acts as a hydrogen-bond acceptor, whereas the hydroxyl group acts as a hydrogen-bond donor. These vibrational modes have different properties depending on their respective chemical bonds, suggesting that hydrogen bonding may have different mechanisms and effects on the VER of the CO and OH modes than previously understood. The IR pump-probe signals of the CO stretching mode of 9-fluorenone and methyl acetate in alcohol, as well as that of acetic acid in water, include several components with different time constants. Quantum chemical calculations indicate that the dynamical components are the result of various hydrogen-bonded complexes that form between solute and solvent molecules. The acceleration of the VER is due to the increasing vibrational density of states caused by the formation of hydrogen bonds. The vibrational dynamics of the OH stretching mode in hydrogen-bonded complexes were studied in several systems. For phenol-base complexes, the decay time constant of the pump-probe signal decreases as the band peak of the IR absorption spectrum shifts to lower wavenumbers (the result of changing the proton acceptor). For phenol oligomers, the decay time constant of the pump-probe signal decreases as the probe wavenumber decreases. These observations show that the VER time strongly correlates with the strength of hydrogen bonding. This acceleration may be due to increased coupling between the OH stretching mode and the accepting mode of the VER, because the low-frequency shift caused by hydrogen bond formation is very large. Unlike phenol oligomers, however, the pump-probe signals of phenol-base complexes did not exhibit probe frequency dependence. For these complexes, rapid interconversion between different conformations causes rapid fluctuations in the vibrational frequency of the OH stretching modes, and these fluctuations level the VER times of different conformations. For the benzoic acid dimer, a quantum beat at a frequency of around 100 cm(-1) is superimposed on the pump-probe signal. This result indicates the presence of strong anharmonic coupling between the intramolecular OH stretching and the intermolecular stretching modes. From a two-dimensional plot of the OH stretching wavenumber and the low-frequency wavenumber, the wavenumber of the low-frequency mode is found to increase monotonically as the probe wavenumber is shifted toward lower wavenumbers. Our results represent a quantitative determination of the acceleration of VER by the formation of hydrogen bonds. Our studies merit further evaluation and raise fundamental questions about the current theory of vibrational dynamics in the condensed phase.

2,4-Dinitrophenylhydrazine, redetermined at 120 K: a three-dimensional framework built from N-H...O, N-H...(O)2, N-H...pi(arene) and C-H...O hydrogen bonds.

PubMed

Wardell, James L; Low, John N; Glidewell, Christopher

2006-06-01

In the title compound, C6H6N4O4, the bond distances indicate significant bond fixation, consistent with charge-separated polar forms. The molecules are almost planar and there is an intramolecular N-H...O hydrogen bond. The molecules are linked into a complex three-dimensional framework structure by a combination of N-H...O, N-H...(O)2, N-H...pi(arene) and C-H...O hydrogen bonds.

Nature and potency interactions of the hydrogen bond through the NBO analysis for charge transfer complex between 2-amino-4-hydroxy-6-methylpyrimidine and 2,3-pyrazinedicarboxylic acid

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Afroz, Ziya; Alam, Mohammad Jane; Bhat, Sheeraz Ahmad; Ahmad, Shabbir; Ahmad, Afaq

2018-05-01

The intermolecular interactions in complex formation between 2-amino-4-hydroxy-6-methylpyrimidine (AHMP) and 2,3-pyrazinedicarboxylicacid (PDCA) have been explored using density functional theory calculations. The isolated 1:1 molecular geometry of proton transfer (PT) complex between AHMP and PDCA has been optimized on a counterpoise corrected potential energy surface (PES) at DFT-B3LYP/6-31G(d,p) level of theory in the gaseous phase. Further, the formation of hydrogen bonded charge transfer (HBCT) complex between PDCA and AHMP has been also discussed. PT energy barrier between two extremes is calculated using potential energy surface (PES) scan by varying bond length. The intermolecular interactions have been analyzed from theoretical perspective of natural bond orbital (NBO) analysis. In addition, the interaction energy between molecular fragments involved in the complex formation has been also computed by counterpoise procedure at same level of theory.

Use of infrared spectroscopy for the determination of electronegativity of rare earth elements.

PubMed

Frost, Ray L; Erickson, Kristy L; Weier, Matt L; McKinnon, Adam R; Williams, Peter A; Leverett, Peter

2004-07-01

Infrared spectroscopy has been used to study a series of synthetic agardite minerals. Four OH stretching bands are observed at around 3568, 3482, 3362, and 3296 cm(-1). The first band is assigned to zeolitic, non-hydrogen-bonded water. The band at 3296 cm(-1) is assigned to strongly hydrogen-bonded water with an H bond distance of 2.72 A. The water in agardites is better described as structured water and not as zeolitic water. Two bands at around 999 and 975 cm(-1) are assigned to OH deformation modes. Two sets of AsO symmetric stretching vibrations were found and assigned to the vibrational modes of AsO(4) and HAsO(4) units. Linear relationships between positions of infrared bands associated with bonding to the OH units and the electronegativity of the rare earth elements were derived, with correlation coefficients >0.92. These linear functions were then used to calculate the electronegativity of Eu, for which a value of 1.1808 on the Pauling scale was found.

Comprehensive physicochemical studies of a new hybrid material: 2-Amino-4-methyl-3-nitropyridinium hydrogen oxalate

NASA Astrophysics Data System (ADS)

Bryndal, I.; Kucharska, E.; Wandas, M.; Lorenc, J.; Hermanowicz, K.; Mączka, M.; Lis, T.; Marchewka, M.; Hanuza, J.

2014-01-01

A new organic-organic salt, 2-amino-4-methyl-3-nitropyridinium hydrogen oxalate (AMNPO), and its deuterium analogue have been synthesized and characterized by means of FT-IR, FT-Raman, DSC and single crystal X-ray studies. The DSC measurements and temperature dependence of the IR and Raman spectra in the range 4-295 K show that it undergoes a reversible phase transition at ∼240 K. At room temperature it crystallizes in noncentrosymmetric space group P21. The unit-cell is built of the 2-amino-4-methyl-3-nitropyridinium cations and oxalate monoanions which are connected via the Nsbnd H⋯O and Osbnd H⋯O hydrogen bonds. The geometrical and hydrogen bond parameters are similar for non-deuterated (at 120 and 293 K) and deuterated compounds (at 90 K). The phase transition is probably a consequence of order-disorder transition inside of hydrogen network. The 6-311G(2d,2p) basis set with B3LYP functional have been used to discuss the structure and vibrational spectra of the studied compound.

The nature of three-body interactions in DFT: Exchange and polarization effects

NASA Astrophysics Data System (ADS)

Hapka, Michał; Rajchel, Łukasz; Modrzejewski, Marcin; Schäffer, Rainer; Chałasiński, Grzegorz; Szcześniak, Małgorzata M.

2017-08-01

We propose a physically motivated decomposition of density functional theory (DFT) 3-body nonadditive interaction energies into the exchange and density-deformation (polarization) components. The exchange component represents the effect of the Pauli exclusion in the wave function of the trimer and is found to be challenging for density functional approximations (DFAs). The remaining density-deformation nonadditivity is less dependent upon the DFAs. Numerical demonstration is carried out for rare gas atom trimers, Ar2-HX (X = F, Cl) complexes, and small hydrogen-bonded and van der Waals molecular systems. None of the tested semilocal, hybrid, and range-separated DFAs properly accounts for the nonadditive exchange in dispersion-bonded trimers. By contrast, for hydrogen-bonded systems, range-separated DFAs achieve a qualitative agreement to within 20% of the reference exchange energy. A reliable performance for all systems is obtained only when the monomers interact through the Hartree-Fock potential in the dispersion-free Pauli blockade scheme. Additionally, we identify the nonadditive second-order exchange-dispersion energy as an important but overlooked contribution in force-field-like dispersion corrections. Our results suggest that range-separated functionals do not include this component, although semilocal and global hybrid DFAs appear to imitate it in the short range.

Photoinduced Intramolecular Bifurcate Hydrogen Bond: Unusual Mutual Influence of the Components.

PubMed

Sigalov, Mark V; Shainyan, Bagrat A; Sterkhova, Irina V

2017-09-01

A series of 7-hydroxy-2-methylidene-2,3-dihydro-1H-inden-1-ones with 2-pyrrolyl (3), 4-dimethylaminophenyl (4), 4-nitrophenyl (5), and carboxyl group (6) as substituents at the exocyclic double bond was synthesized in the form of the E-isomers (4-6) or predominantly as the Z-isomer (3) which in solution is converted to the E-isomer. The synthesized compounds and their model analogues were studied by NMR spectroscopy, X-ray analysis, and MP2 theoretical calculations. The E-isomers having intramolecular O-H···O═C hydrogen bond are converted by UV irradiation to the Z-isomers having bifurcated O-H···O···H-X hydrogen bond. Unexpected shortening (and, thus, strengthening) of the O-H···O═C component of the bifurcated hydrogen bond upon the formation of the C═O···H-X hydrogen bond was found experimentally, proved theoretically (MP2), and explained by a roundabout interaction of the H-donor (HX) and H-acceptor (C═O) via the system of conjugated bonds.

Hydrogen bonding: part 78. Ab initio molecular orbital study of intra- and intermolecular hydrogen bonding in choline and betaine and their compounds with HF and H 2O

NASA Astrophysics Data System (ADS)

Harmon, K. M.; Avci, G. F.; Madeira, S. L.; Mounts, P. A.; Thiel, A. C.

2001-10-01

We previously prepared several compounds of the zwitterions [(CH3)3NCH2CH2O]0 (deprotonated choline, herein named cholaine) and [(CH3)3NCH2CO2]0 (betaine) and proposed structures based on infrared spectroscopy. We now examine these compounds with use of ab initio molecular orbital methods to further elucidate possible structure. These calculations demonstrate that: (1) cholaine and betaine both have internal CHO hydrogen bonds, and these are retained in some form in all other compounds. (2) Cholaine hydrate and hydrofluoride and betaine hydrofluoride monomers have covalent three-center hydrogen bonds between H2O or HF and negative zwitterion oxygen, and additional CHX hydrogen bonds to H2O oxygen or HF fluorine. (3) Cholaine monohydrate and cholaine hydrofluoride monohydrate form dimers of Ci symmetry which contain planar C2h (H2O·O)2 and (HOH·F)2 clusters. (4) Cholaine hydrofluoride forms head-to-tail dimers bound by intermolecular CHX hydrogen bonds; this arrangement could lead to extended linear structures in the solid state. (5) Betaine hydrofluoride, in contrast, forms a tightly bound discrete dimeric unit in which two molecules join in a head-to-head manner held together by five intermolecular hydrogen bonds and by the mutual proximities of negative fluorides to positive nitrogens.

Structure of saligenin: microwave, UV and IR spectroscopy studies in a supersonic jet combined with quantum chemistry calculations.

PubMed

Kumar, Sumit; Singh, Santosh K; Calabrese, Camilla; Maris, Assimo; Melandri, Sonia; Das, Aloke

2014-08-28

In this study, we have determined the structure of a medicinally important molecule saligenin (2-hydroxybenzyl alcohol) using UV, IR and microwave absorption spectroscopy in a supersonic jet combined with ab initio calculations. The structure of the only observed conformer of saligenin corresponds to the global minimum on the conformational surface. The observed structure is stabilized by an intramolecular strong O-H···O hydrogen bonding as well as a very weak O-H···π interaction. The hydrogen bond is formed through phenolic OH as the hydrogen bond donor and benzylic OH as the hydrogen bond acceptor while the O-H···π interaction is through benzylic O-H as the hydrogen bond donor and phenyl group as the hydrogen bond acceptor. It has been observed that the benzylic OH stretching frequency in saligenin is more red-shifted compared to that in benzyl alcohol as the strong O-H···O interaction present in saligenin acts on the benzylic O-H group. In fact, there is a subtle interplay among the strong O-H···O hydrogen bond, weak O-H···π interaction, and steric effects arising from the ortho substitution of the OH group in benzyl alcohol. This fine-tuning of multiple interactions very often governs the specific structures of biomolecules and materials.

How many hydrogen-bonded α-turns are possible?

PubMed

Schreiber, Anette; Schramm, Peter; Hofmann, Hans-Jörg

2011-06-01

The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311 + G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i + 4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i + 4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an "ideal" α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the C(α)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i + 4) hydrogen bond.

Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions.

PubMed

Milenkovic, Stefan; Bondar, Ana-Nicoleta

2016-02-01

SecA uses the energy yielded by the binding and hydrolysis of adenosine triphosphate (ATP) to push secretory pre-proteins across the plasma membrane in bacteria. Hydrolysis of ATP occurs at the nucleotide-binding site, which contains the conserved carboxylate groups of the DEAD-box helicases. Although crystal structures provide valuable snapshots of SecA along its reaction cycle, the mechanism that ensures conformational coupling between the nucleotide-binding site and the other domains of SecA remains unclear. The observation that SecA contains numerous hydrogen-bonding groups raises important questions about the role of hydrogen-bonding networks and hydrogen-bond dynamics in long-distance conformational couplings. To address these questions, we explored the molecular dynamics of SecA from three different organisms, with and without bound nucleotide, in water. By computing two-dimensional hydrogen-bonding maps we identify networks of hydrogen bonds that connect the nucleotide-binding site to remote regions of the protein, and sites in the protein that respond to specific perturbations. We find that the nucleotide-binding site of ADP-bound SecA has a preferred geometry whereby the first two carboxylates of the DEAD motif bridge via hydrogen-bonding water. Simulations of a mutant with perturbed ATP hydrolysis highlight the water-bridged geometry as a key structural element of the reaction path. Copyright © 2015. Published by Elsevier B.V.

Structure and physicochemical characterization of a naproxen–picolinamide cocrystal

PubMed Central

Kerr, Hannah E.; Softley, Lorna K.; Suresh, Kuthuru; Hodgkinson, Paul; Evans, Ivana Radosavljevic

2017-01-01

Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-meth­oxy­naphthalen-2-yl)propanoic acid–pyridine-2-carbox­amide (1/1), C14H14O3·C6H6N2O]. The pharmaceutically relevant physical properties were investigated and the intrinsic dissolution rate was found to be essentially the same as that of commercial naproxen. An NMR crystallography approach was used to investigate the H-atom positions in the two crystallographically unique COOH–CONH hydrogen-bonded dimers. 1H solid-state NMR distinguished the two carboxyl protons, despite the very similar crystallographic environments. The nature of the hydrogen bonding was confirmed by solid-state NMR and density functional theory calculations. PMID:28257010

Structure and physicochemical characterization of a naproxen-picolinamide cocrystal.

PubMed

Kerr, Hannah E; Softley, Lorna K; Suresh, Kuthuru; Hodgkinson, Paul; Evans, Ivana Radosavljevic

2017-03-01

Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-methoxynaphthalen-2-yl)propanoic acid-pyridine-2-carboxamide (1/1), C 14 H 14 O 3 ·C 6 H 6 N 2 O]. The pharmaceutically relevant physical properties were investigated and the intrinsic dissolution rate was found to be essentially the same as that of commercial naproxen. An NMR crystallography approach was used to investigate the H-atom positions in the two crystallographically unique COOH-CONH hydrogen-bonded dimers. 1 H solid-state NMR distinguished the two carboxyl protons, despite the very similar crystallographic environments. The nature of the hydrogen bonding was confirmed by solid-state NMR and density functional theory calculations.

Quantitative analysis of desorption and decomposition kinetics of formic acid on Cu(111): The importance of hydrogen bonding between adsorbed species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shiozawa, Yuichiro; Koitaya, Takanori; Mukai, Kozo

2015-12-21

Quantitative analysis of desorption and decomposition kinetics of formic acid (HCOOH) on Cu(111) was performed by temperature programmed desorption (TPD), X-ray photoelectron spectroscopy, and time-resolved infrared reflection absorption spectroscopy. The activation energy for desorption is estimated to be 53–75 kJ/mol by the threshold TPD method as a function of coverage. Vibrational spectra of the first layer HCOOH at 155.3 K show that adsorbed molecules form a polymeric structure via the hydrogen bonding network. Adsorbed HCOOH molecules are dissociated gradually into monodentate formate species. The activation energy for the dissociation into monodentate formate species is estimated to be 65.0 kJ/mol atmore » a submonolayer coverage (0.26 molecules/surface Cu atom). The hydrogen bonding between adsorbed HCOOH species plays an important role in the stabilization of HCOOH on Cu(111). The monodentate formate species are stabilized at higher coverages, because of the lack of vacant sites for the bidentate formation.« less

Probing hydrogen bond networks in half-sandwich Ru(II) building blocks by a combined 1H DQ CRAMPS solid-state NMR, XRPD, and DFT approach.

PubMed

Chierotti, Michele R; Gobetto, Roberto; Nervi, Carlo; Bacchi, Alessia; Pelagatti, Paolo; Colombo, Valentina; Sironi, Angelo

2014-01-06

The hydrogen bond network of three polymorphs (1α, 1β, and 1γ) and one solvate form (1·H2O) arising from the hydration-dehydration process of the Ru(II) complex [(p-cymene)Ru(κN-INA)Cl2] (where INA is isonicotinic acid), has been ascertained by means of one-dimensional (1D) and two-dimensional (2D) double quantum (1)H CRAMPS (Combined Rotation and Multiple Pulses Sequences) and (13)C CPMAS solid-state NMR experiments. The resolution improvement provided by homonuclear decoupling pulse sequences, with respect to fast MAS experiments, has been highlighted. The solid-state structure of 1γ has been fully characterized by combining X-ray powder diffraction (XRPD), solid-state NMR, and periodic plane-wave first-principles calculations. None of the forms show the expected supramolecular cyclic dimerization of the carboxylic functions of INA, because of the presence of Cl atoms as strong hydrogen bond (HB) acceptors. The hydration-dehydration process of the complex has been discussed in terms of structure and HB rearrangements.

Use of π-π forces to steer the assembly of a NTA complex of Cu(II) into hydrogen bonded supramolecular layers (H 3NTA = nitrilotriacetic acid)

NASA Astrophysics Data System (ADS)

Dey, Biswajit; Choudhury, Somnath Ray; Suresh, Eringathodi; Jana, Atish Dipankar; Mukhopadhyay, Subrata

2009-03-01

We propose a crystal engineering principle where we show that it might be possible to direct the organization of molecular complexes into hydrogen bonded supramolecular layers through the use of suitable co-ligands possessing both the hydrogen-bonding as well as π-π stacking capability. This principle has been tested for the organization of [Cu(NTA) 2] units (H 3NTA = nitrilotriacetic acid, N(CH 2CO 2H) 3) in the molecular complex with formula (2-A-PH) 4[Cu(NTA) 2]·6H 2O ( 1), where 2-A-PH is protonated 2-amino-4-picoline. In 1, the 2-amino-4-picoline co-ligands have been utilized to direct the organization of [Cu(NTA) 2] units into hydrogen bonded layers. The linear stacking of π-π bonded protonated 2-amino-4-picoline molecules can be thought as the influencing agent for the organization of [Cu(NTA) 2] units into hydrogen bonded layers.

Interstellar hydrogen bonding

NASA Astrophysics Data System (ADS)

Etim, Emmanuel E.; Gorai, Prasanta; Das, Ankan; Chakrabarti, Sandip K.; Arunan, Elangannan

2018-06-01

This paper reports the first extensive study of the existence and effects of interstellar hydrogen bonding. The reactions that occur on the surface of the interstellar dust grains are the dominant processes by which interstellar molecules are formed. Water molecules constitute about 70% of the interstellar ice. These water molecules serve as the platform for hydrogen bonding. High level quantum chemical simulations for the hydrogen bond interaction between 20 interstellar molecules (known and possible) and water are carried out using different ab-intio methods. It is evident that if the formation of these species is mainly governed by the ice phase reactions, there is a direct correlation between the binding energies of these complexes and the gas phase abundances of these interstellar molecules. Interstellar hydrogen bonding may cause lower gas abundance of the complex organic molecules (COMs) at the low temperature. From these results, ketenes whose less stable isomers that are more strongly bonded to the surface of the interstellar dust grains have been observed are proposed as suitable candidates for astronomical observations.

A systemic investigation of hydrogen peroxide clusters (H2O2)n (n = 1-6) and liquid-state hydrogen peroxide: based on atom-bond electronegativity equalization method fused into molecular mechanics and molecular dynamics.

PubMed

Yu, Chun-Yang; Yang, Zhong-Zhi

2011-03-31

Hydrogen peroxide (HP) clusters (H(2)O(2))(n) (n = 1-6) and liquid-state HP have been systemically investigated by the newly constructed ABEEM/MM fluctuating charge model. Because of the explicit description of charge distribution and special treatment of the hydrogen-bond interaction region, the ABEEM/MM potential model gives reasonable properties of HP clusters, including geometries, interaction energies, and dipole moments, when comparing with the present ab initio results. Meanwhile, the average dipole moment, static dielectric constant, heats of vaporization, radial distribution function, and diffusion constant for the dynamic properties of liquid HP at 273 K and 1 atm are fairly consistent with the available experimental data. To the best of our knowledge, this is the first theoretical investigation of condensed HP. The properties of HP monomer are studied in detail involving the structure, torsion potentials, molecular orbital analysis, charge distribution, dipole moment, and vibrational frequency.

Ratio of entropy to enthalpy in thermal transitions in biological tissues.

PubMed

Jacques, Steven L

2006-01-01

Thermal transitions in biological tissues that have been reported in the literature are summarized in terms of the apparent molar entropy (DeltaS) and molar enthalpy (DeltaH) involved in the transition. A plot of DeltaS versus DeltaH for all the data yields a straight line, consistent with the definition of free energy, DeltaG=DeltaH+TDeltaS. Various bonds may be involved in cooperative bond breakage during thermal transitions; however, for the sake of description, the equivalent number of cooperative hydrogen bonds can be cited. Most of the tissue data behave as if 10 to 20 hydrogen bonds are cooperatively broken during coagulation, with one transition, the expression of heat shock protein, involving 90 cooperative hydrogen bonds. The data are consistent with DeltaS=a+bDeltaH, where a=-327.5 J(mol K) and b=31.47 x 10(-4) K(-1). If each additional hydrogen bond adds 19 x 10(3) Jmol to DeltaH, then each additional bond adds 59.8 J(mol K) to DeltaS. Hence, the dynamics of irreversible thermal transitions can be described in terms of one free parameter, the apparent number of cooperative hydrogen bonds broken during the transition.

Catalytic Carbonyl Allylation, Propargylation and Vinylation from the Alcohol or Aldehyde Oxidation Level via C-C Bond Forming Hydrogenation and Transfer Hydrogenation: A Departure from Preformed Organometallic Reagents**

PubMed Central

Bower, John F.; Kim, In Su; Patman, Ryan L.; Krische, Michael J.

2009-01-01

Classical protocols for carbonyl allylation, propargylation and vinylation typically rely upon the use of preformed allyl metal, allenyl metal and vinyl metal reagents, respectively, mandating stoichiometric generation of metallic byproducts. Through transfer hydrogenative C-C coupling, carbonyl addition may be achieved from the aldehyde or alcohol oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. Here, we review transfer hydrogenative methods for carbonyl addition, which encompass the first cataltyic protocols enabling direct C–H functionalization of alcohols. PMID:19040235

Probing the Low-Barrier Hydrogen Bond in Hydrogen Maleate in the Gas Phase: A Photoelectron Spectroscopy and ab Initio Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woo, Hin-koon; Wang, Xue B.; Wang, Lai S.

2005-12-01

The strength of the low-barrier hydrogen bond in hydrogen maleate in the gas phase was investigated by low-temperature photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of maleic and fumaric acid monoanions (cis-/trans-HO2CCHdCHCO2 -) were obtained at low temperatures and at 193 nm photon energy. Vibrational structure was observed for trans-HO2CCHdCHCO2 - due to the OCO bending modes; however, cis-HO2CCHdCHCO2 - yielded a broad and featureless spectrum. The electron binding energy of cis-HO2CCHdCHCO2 - is about 1 eV blue-shifted relative to trans-HO2CCHdCHCO2 - due to the formation of intramolecular hydrogen bond in the cis-isomer. Theoretical calculations (CCSD(T)/ aug-cc-pVTZ and B3LYP/aug-cc-pVTZ)more » were carried out to estimate the strength of the intramolecular hydrogen bond in cis-HO2CCHdCHCO2 -. Combining experimental and theoretical calculations yields an estimate of 21.5 ( 2.0 kcal/mol for the intramolecular hydrogen bond strength in hydrogen maleate.« less

Aryl C—H···Cl– Hydrogen Bonding in a Fluorescent Anion Sensor

PubMed Central

Tresca, Blakely W.; Zakharov, Lev N.; Carroll, Calden N.; Johnson, Darren W.; Haley, Michael M.

2014-01-01

A new phenyl-acetylene receptor containing a carbonaceous hydrogen bond donor activates anion binding in conjunction with two stabilizing ureas. The unusual CH···Cl– hydrogen bond is apparent in solution by large 1H NMR chemical shifts and by a short, linear contact in the solid state. PMID:23843050

Investigating Hydrogen Bonding in Phenol Using Infrared Spectroscopy and Computational Chemistry

ERIC Educational Resources Information Center

Fedor, Anna M.; Toda, Megan J.

2014-01-01

The hydrogen bonding of phenol can be used as an introductory model for biological systems because of its structural similarities to tyrosine, a para-substituted phenol that is an amino acid essential to the synthesis of proteins. Phenol is able to form hydrogen bonds readily in solution, which makes it a suitable model for biological…

Statics and dynamics of free and hydrogen-bonded OH groups at the air/water interface.

PubMed

Vila Verde, Ana; Bolhuis, Peter G; Campen, R Kramer

2012-08-09

We use classical atomistic molecular dynamics simulations of two water models (SPC/E and TIP4P/2005) to investigate the orientation and reorientation dynamics of two subpopulations of OH groups belonging to water molecules at the air/water interface at 300 K: those OH groups that donate a hydrogen bond (called "bonded") and those that do not (called "free"). Free interfacial OH groups reorient in two distinct regimes: a fast regime from 0 to 1 ps and a slow regime thereafter. Qualitatively similar behavior was reported by others for free OH groups near extended hydrophobic surfaces. In contrast, the net reorientation of bonded OH groups occurs at a rate similar to that of bulk water. This similarity in reorientation rate results from compensation of two effects: decreasing frequency of hydrogen-bond breaking/formation (i.e., hydrogen-bond exchange) and faster rotation of intact hydrogen bonds. Both changes result from the decrease in density at the air/water interface relative to the bulk. Interestingly, because of the presence of capillary waves, the slowdown of hydrogen-bond exchange is significantly smaller than that reported for water near extended hydrophobic surfaces, but it is almost identical to that reported for water near small hydrophobic solutes. In this sense water at the air/water interface has characteristics of water of hydration of both small and extended hydrophobic solutes.

Turn-Directed α-β Conformational Transition of α-syn12 Peptide at Different pH Revealed by Unbiased Molecular Dynamics Simulations

PubMed Central

Liu, Lei; Cao, Zanxia

2013-01-01

The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn9-6 and four hydrogen bonds (HB9-6, HB6-9, HB11-4 and HB4-11) are formed at physiological pH; turn8-5 and five hydrogen bonds (HB8-5, HB5-8, HB10-3, HB3-10 and HB12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn5-2 firstly, followed by the formation of part hydrogen bonds, then turn5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH. PMID:23708094