Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

PubMed

Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

2016-09-21

Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc. At the other end of the spectrum is another computational approach: modern ab initio Valence Bond Theory (VBT). VBT differs from molecular orbital theory based methods in the expression of the molecular wave function. The molecular wave function in the valence bond ansatz is expressed as a linear combination of valence bond structures. These structures include covalent and ionic structures explicitly. Modern ab initio valence bond theory calculations of representative primary and tertiary ammonium protic ionic liquids indicate that modern ab initio valence bond theory can be employed to assess the acidity and ionicity of protic ionic liquids a priori.

Nonorthogonal orbital based N-body reduced density matrices and their applications to valence bond theory. I. Hamiltonian matrix elements between internally contracted excited valence bond wave functions

NASA Astrophysics Data System (ADS)

Chen, Zhenhua; Chen, Xun; Wu, Wei

2013-04-01

In this series, the n-body reduced density matrix (n-RDM) approach for nonorthogonal orbitals and their applications to ab initio valence bond (VB) methods are presented. As the first paper of this series, Hamiltonian matrix elements between internally contracted VB wave functions are explicitly provided by means of nonorthogonal orbital based RDM approach. To this end, a more generalized Wick's theorem, called enhanced Wick's theorem, is presented both in arithmetical and in graphical forms, by which the deduction of expressions for the matrix elements between internally contracted VB wave functions is dramatically simplified, and the matrix elements are finally expressed in terms of tensor contractions of electronic integrals and n-RDMs of the reference VB self-consistent field wave function. A string-based algorithm is developed for the purpose of evaluating n-RDMs in an efficient way. Using the techniques presented in this paper, one is able to develop new methods and efficient algorithms for nonorthogonal orbital based many-electron theory much easier than by use of the first quantized formulism.

Enhancing Adhesion: Relative Merits of Different Approaches

NASA Technical Reports Server (NTRS)

Penn, L. S.; Pater, R.

1996-01-01

Adhesive performance is improved mainly by manipulation of the bimaterials interface zone, which is only a few molecules thick. There are three approaches to enhancement of interfacial adhesion at the molecular level. They are 1) changing the nonchemically bonded interactions across the interface from weak ones to strong ones, 2) making the true interfacial area much larger than the simple geometric area, and 3) inducing chemical bonding between the two materials forming the interface. Our goal this summer was to question some of the built-in assumptions contained within these approaches and to determine the most promising approach, both theoretically and practically, for enhancing adhesion in NASA structures. Our computations revealed that all three of these approaches have, in theory, the potential to enhance molecular adhesion approximately ten-fold. Experiments, however, revealed that this excellent level of enhancement is not likely to be reached in practice. Each approach was found to be severely limited by practical problems. In addition, some of the built-in assumptions associated with these approaches were found to be insufficient or inadequate. The first approach, changing the nonchemically bonded interactions from weak to strong, Is an example of one containing inadequate assumptions. The extensive literature on intermolecular interactions, based on solution studies, shows that certain functional group pairs interact much more strongly than others. It has always been assumed that these data can be reliably extended to systems where only one member of the pair is in solution and the other Is contained in a solid surface. Our experiments this summer demonstrated that solution data do not adequately predict the strength of functional group interaction at the solid-liquid interface. Furthermore, the strong solvents needed to dissolve the monomers or polymers to which the functional groups of interest are attached compete successfully with the solid surface for the functional group. As a result, functional groups in solution cannot pair with the complementary groups in the solid surface, and the expected enhancement of nonchemically bonded interactions is not realized. The second approach, increasing the true interfacial area, is an example of one containing inadequate assumptions and suffering from numerous practical problems. First, practitioners have assumed that material removal, such as bead blasting or etching, increases true surface area (and therefore interfacial area) in a meaningful way. Our geometric analysis demonstrated that removal methods increase area by a factor of two at most. To increase interfacial area by an order of magnitude or more. a thin layer of high porosity must be added to the substrate surface prior to application of the adhesive phase. Consistent with this finding, we attempted to create a thin layer of rigid, highly porous glass on the surface of our smooth glass substrate by means of sol-gel technology. We were unable to surmount a wide variety of practical problems and obtained only collapsed, nonporous layers. Thus this approach, appealing in principle, would require long term development and is not promising in the near term. The third approach, inducing chemical bonding at the interface, is an example of one having neither inadequate assumptions nor insurmountable practical problems. When silicate glass is the substrate, there are only a few chemical reactions that can be successfully conducted to create these chemical bonds, and these reactions usually involve silicon-containing reagents. We compared the silazane reagents to the silane reagents and found through experiment that the silazanes react with the glass surface much more readily, and under milder conditions, than the silanes. The functional groups attached to the glass surface by silazane reactions were not able to be removed by solvent extraction, elevated temperature exposure, or mechanical action. This clearly indicates that the formation of chemical bonds at the interface is the most effective approach for enhancing molecular adhesion.

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.

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

Numerical investigation of compaction of deformable particles with bonded-particle model

NASA Astrophysics Data System (ADS)

Dosta, Maksym; Costa, Clara; Al-Qureshi, Hazim

2017-06-01

In this contribution, a novel approach developed for the microscale modelling of particles which undergo large deformations is presented. The proposed method is based on the bonded-particle model (BPM) and multi-stage strategy to adjust material and model parameters. By the BPM, modelled objects are represented as agglomerates which consist of smaller ideally spherical particles and are connected with cylindrical solid bonds. Each bond is considered as a separate object and in each time step the forces and moments acting in them are calculated. The developed approach has been applied to simulate the compaction of elastomeric rubber particles as single particles or in a random packing. To describe the complex mechanical behaviour of the particles, the solid bonds were modelled as ideally elastic beams. The functional parameters of solid bonds as well as material parameters of bonds and primary particles were estimated based on the experimental data for rubber spheres. Obtained results for acting force and for particle deformations during uniaxial compression are in good agreement with experimental data at higher strains.

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

The Heats of Formation of GaCl3 and its Fragments

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

1998-01-01

The heats of formation of GaC13 and its fragments are computed. The geometries and frequencies are obtained at the B3LYP level. The CCSD(T) approach is used to solve the correlation problem. The effect of Ga 3d correlation is studied, and found to affect the bond energies by up to 1 kcal/mol. Both basis set extrapolation and bond functions are considered as ways to approach the basis set limit. Spin-orbit and scalar relativistic effects are also considered.

Nanoparticle/Polymer Nanocomposite Bond Coat or Coating

NASA Technical Reports Server (NTRS)

Miller, Sandi G.

2011-01-01

This innovation addresses the problem of coatings (meant to reduce gas permeation) applied to polymer matrix composites spalling off in service due to incompatibility with the polymer matrix. A bond coat/coating has been created that uses chemically functionalized nanoparticles (either clay or graphene) to create a barrier film that bonds well to the matrix resin, and provides an outstanding barrier to gas permeation. There is interest in applying clay nanoparticles as a coating/bond coat to a polymer matrix composite. Often, nanoclays are chemically functionalized with an organic compound intended to facilitate dispersion of the clay in a matrix. That organic modifier generally degrades at the processing temperature of many high-temperature polymers, rendering the clay useless as a nano-additive to high-temperature polymers. However, this innovation includes the use of organic compounds compatible with hightemperature polymer matrix, and is suitable for nanoclay functionalization, the preparation of that clay into a coating/bondcoat for high-temperature polymers, the use of the clay as a coating for composites that do not have a hightemperature requirement, and a comparable approach to the preparation of graphene coatings/bond coats for polymer matrix composites.

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.

Fixed-Node Diffusion Quantum Monte Carlo Method on Dissociation Energies and Their Trends for R-X Bonds (R = Me, Et, i-Pr, t-Bu).

PubMed

Hou, Aiqiang; Zhou, Xiaojun; Wang, Ting; Wang, Fan

2018-05-15

Achieving both bond dissociation energies (BDEs) and their trends for the R-X bonds with R = Me, Et, i-Pr, and t-Bu reliably is nontrivial. Density functional theory (DFT) methods with traditional exchange-correlation functionals usually have large error on both the BDEs and their trends. The M06-2X functional gives rise to reliable BDEs, but the relative BDEs are determined not as accurately. More demanding approaches such as some double-hybrid functionals, for example, G4 and CCSD(T), are generally required to achieve the BDEs and their trends reliably. The fixed-node diffusion quantum Monte Carlo method (FN-DMC) is employed to calculated BDEs of these R-X bonds with X = H, CH 3 , OCH 3 , OH, and F in this work. The single Slater-Jastrow wave function is adopted as trial wave function, and pseudopotentials (PPs) developed for quantum Monte Carlo calculations are chosen. Error of these PPs is modest in wave function methods, while it is more pronounced in DFT calculations. Our results show that accuracy of BDEs with FN-DMC is similar to that of M06-2X and G4, and trends in BDEs are calculated more reliably than M06-2X. Both BDEs and trends in BDEs of these bonds are reproduced reasonably with FN-DMC. FN-DMC using PPs can thus be applied to BDEs and their trends of similar chemical bonds in larger molecules reliably and provide valuable information on properties of these molecules.

Wire-bonder-assisted integration of non-bondable SMA wires into MEMS substrates

NASA Astrophysics Data System (ADS)

Fischer, A. C.; Gradin, H.; Schröder, S.; Braun, S.; Stemme, G.; van der Wijngaart, W.; Niklaus, F.

2012-05-01

This paper reports on a novel technique for the integration of NiTi shape memory alloy wires and other non-bondable wire materials into silicon-based microelectromechanical system structures using a standard wire-bonding tool. The efficient placement and alignment functions of the wire-bonding tool are used to mechanically attach the wire to deep-etched silicon anchoring and clamping structures. This approach enables a reliable and accurate integration of wire materials that cannot be wire bonded by traditional means.

Csbnd N bond formation in alicyclic and heterocyclic compounds by amine-modified nanoclay

NASA Astrophysics Data System (ADS)

Zarnegar, Zohre; Alizadeh, Roghayeh; Ahmadzadeh, Majid; Safari, Javad

2017-09-01

In the current protocol, amine functionalized montmorillonite K10 nanoclay (NH2-MMT) was applied to catalyze the formation of Csbnd N bonds in the synthesis of azines and 2-aminothiazoles at room temperature. In comparison with the current methods of Csbnd N bond formation, this approach displays specific advantages include atom economy, clean conversion, design for energy efficiency, the use of nontoxic and heterogeneous catalyst, higher purity and yields, safer solvent and reagents for this organic transformation.

Site-selective and stereoselective functionalization of non-activated tertiary C-H bonds

NASA Astrophysics Data System (ADS)

Liao, Kuangbiao; Pickel, Thomas C.; Boyarskikh, Vyacheslav; Bacsa, John; Musaev, Djamaladdin G.; Davies, Huw M. L.

2017-11-01

The synthesis of complex organic compounds usually relies on controlling the reactions of the functional groups. In recent years, it has become possible to carry out reactions directly on the C-H bonds, previously considered to be unreactive. One of the major challenges is to control the site-selectivity because most organic compounds have many similar C-H bonds. The most well developed procedures so far rely on the use of substrate control, in which the substrate has one inherently more reactive C-H bond or contains a directing group or the reaction is conducted intramolecularly so that a specific C-H bond is favoured. A more versatile but more challenging approach is to use catalysts to control which site in the substrate is functionalized. p450 enzymes exhibit C-H oxidation site-selectivity, in which the enzyme scaffold causes a specific C-H bond to be functionalized by placing it close to the iron-oxo haem complex. Several studies have aimed to emulate this enzymatic site-selectivity with designed transition-metal catalysts but it is difficult to achieve exceptionally high levels of site-selectivity. Recently, we reported a dirhodium catalyst for the site-selective functionalization of the most accessible non-activated (that is, not next to a functional group) secondary C-H bonds by means of rhodium-carbene-induced C-H insertion. Here we describe another dirhodium catalyst that has a very different reactivity profile. Instead of the secondary C-H bond, the new catalyst is capable of precise site-selectivity at the most accessible tertiary C-H bonds. Using this catalyst, we modify several natural products, including steroids and a vitamin E derivative, indicating the applicability of this method of synthesis to the late-stage functionalization of complex molecules. These studies show it is possible to achieve site-selectivity at different positions within a substrate simply by selecting the appropriate catalyst. We hope that this work will inspire the design of even more sophisticated catalysts, such that catalyst-controlled C-H functionalization becomes a broadly applied strategy for the synthesis of complex molecules.

Low-temperature bonded glass-membrane microfluidic device for in vitro organ-on-a-chip cell culture models

NASA Astrophysics Data System (ADS)

Pocock, Kyall J.; Gao, Xiaofang; Wang, Chenxi; Priest, Craig; Prestidge, Clive A.; Mawatari, Kazuma; Kitamori, Takehiko; Thierry, Benjamin

2015-12-01

The integration of microfluidics with living biological systems has paved the way to the exciting concept of "organson- a-chip", which aims at the development of advanced in vitro models that replicate the key features of human organs. Glass based devices have long been utilised in the field of microfluidics but the integration of alternative functional elements within multi-layered glass microdevices, such as polymeric membranes, remains a challenge. To this end, we have extended a previously reported approach for the low-temperature bonding of glass devices that enables the integration of a functional polycarbonate porous membrane. The process was initially developed and optimised on specialty low-temperature bonding equipment (μTAS2001, Bondtech, Japan) and subsequently adapted to more widely accessible hot embosser units (EVG520HE Hot Embosser, EVG, Austria). The key aspect of this method is the use of low temperatures compatible with polymeric membranes. Compared to borosilicate glass bonding (650 °C) and quartz/fused silica bonding (1050 °C) processes, this method maintains the integrity and functionality of the membrane (Tg 150 °C for polycarbonate). Leak tests performed showed no damage or loss of integrity of the membrane for up to 150 hours, indicating sufficient bond strength for long term cell culture. A feasibility study confirmed the growth of dense and functional monolayers of Caco-2 cells within 5 days.

Low-temperature bonding process for the fabrication of hybrid glass-membrane organ-on-a-chip devices

NASA Astrophysics Data System (ADS)

Pocock, Kyall J.; Gao, Xiaofang; Wang, Chenxi; Priest, Craig; Prestidge, Clive A.; Mawatari, Kazuma; Kitamori, Takehiko; Thierry, Benjamin

2016-10-01

The integration of microfluidics with living biological systems has paved the way to the exciting concept of "organs-on-a-chip," which aims at the development of advanced in vitro models that replicate the key features of human organs. Glass-based devices have long been utilized in the field of microfluidics but the integration of alternative functional elements within multilayered glass microdevices, such as polymeric membranes, remains a challenge. To this end, we have extended a previously reported approach for the low-temperature bonding of glass devices that enables the integration of a functional polycarbonate porous membrane. The process was initially developed and optimized on specialty low-temperature bonding equipment (μTAS2001, Bondtech, Japan) and subsequently adapted to more widely accessible hot embosser units (EVG520HE Hot Embosser, EVG, Austria). The key aspect of this method is the use of low temperatures compatible with polymeric membranes. Compared to borosilicate glass bonding (650°C) and quartz/fused silica bonding (1050°C) processes, this method maintains the integrity and functionality of the membrane (Tg 150°C for polycarbonate). Leak tests performed showed no damage or loss of integrity of the membrane for up to 150 h, indicating sufficient bond strength for long-term cell culture. A feasibility study confirmed the growth of dense and functional monolayers of Caco-2 cells within 5 days.

Effective bond orders from two-step spin–orbit coupling approaches: The I{sub 2}, At{sub 2}, IO{sup +}, and AtO{sup +} case studies

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

Maurice, Rémi, E-mail: remi.maurice@subatech.in2p3.fr; Montavon, Gilles; Réal, Florent

2015-03-07

The nature of chemical bonds in heavy main-group diatomics is discussed from the viewpoint of effective bond orders, which are computed from spin–orbit wave functions resulting from spin–orbit configuration interaction calculations. The reliability of the relativistic correlated wave functions obtained in such two-step spin–orbit coupling frameworks is assessed by benchmark studies of the spectroscopic constants with respect to either experimental data, or state-of-the-art fully relativistic correlated calculations. The I{sub 2}, At{sub 2}, IO{sup +}, and AtO{sup +} species are considered, and differences and similarities between the astatine and iodine elements are highlighted. In particular, we demonstrate that spin–orbit coupling weakensmore » the covalent character of the bond in At{sub 2} even more than electron correlation, making the consideration of spin–orbit coupling compulsory for discussing chemical bonding in heavy (6p) main group element systems.« less

Oxidative 1,2-carboamination of alkenes with alkyl nitriles and amines toward γ-amino alkyl nitriles

NASA Astrophysics Data System (ADS)

Liu, Yan-Yun; Yang, Xu-Heng; Song, Ren-Jie; Luo, Shenglian; Li, Jin-Heng

2017-04-01

Difunctionalization of alkenes has become a powerful tool for quickly increasing molecular complexity in synthesis. Despite significant progress in the area of alkene difunctionalization involving the incorporation of a nitrogen atom across the C-C double bonds, approaches for the direct 1,2-carboamination of alkenes to produce linear N-containing molecules are scarce and remain a formidable challenge. Here we describe a radical-mediated oxidative intermolecular 1,2-alkylamination of alkenes with alkyl nitriles and amines involving C(sp3)-H oxidative functionalization catalysed by a combination of Ag2CO3 with iron Lewis acids. This three-component alkene 1,2-alkylamination method is initiated by the C(sp3)-H oxidative radical functionalization, which enables one-step formation of two new chemical bonds, a C-C bond and a C-N bond, to selectively produce γ-amino alkyl nitriles.

Charging and geometric effects on conduction through Anthracene molecular junctions

NASA Astrophysics Data System (ADS)

Kaur, Rupan Preet; Sawhney, Ravinder Singh; Engles, Derick

We studied the geometric effects on the charge transfer through the anthracenedithiol (ADT) molecular junction using density functional theory combined with the non-equilibrium Green’s function approach. Two major geometric aspects, bond length and bond angle, were moderated to optimize the electrical conduction. From the results established in this paper, we found that the electrical conduction can be tuned from 0.2 G0 to 0.9 G0 by varying the Au-S bond length, whereas the moderation of bonding angle assayed a minor change from 0.37 G0 to 0.47 G0. We attributed this escalating zero bias conductance to the increasing charge on the terminal sulfur atom of the ADT molecule, which increased the energy of the HOMO orbital towards Fermi level and exhibited a semi-metallic behaviour. Therefore, geometry plays a critical role in deciding the charge transport through the metal/molecule interface.

Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.

PubMed

Yilmazer, Nusret Duygu; Korth, Martin

2016-05-16

We review the first successes and failures of a "new wave" of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of "enhanced", dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

‘Umpolung’ Reactivity in Semiaqueous Amide and Peptide Synthesis

PubMed Central

Shen, Bo; Makley, Dawn M.; Johnston, Jeffrey N.

2010-01-01

The amide functional group is one of Nature’s key functional and structural elements, most notably within peptides. Amides are also key intermediates in the preparation of a diverse range of therapeutic small molecules. Its construction using available methods focuses principally upon dehydrative approaches, although oxidative and radical-based methods are representative alternatives. During the carbon-nitrogen bond forming step in most every example, the carbon and nitrogen bear electrophilic and nucleophilic character, respectively. Here we show that activation of amines and nitroalkanes with an electrophilic iodine source in wet THF can lead directly to amide products. Preliminary observations support a mechanistic construct in which reactant polarity is reversed (umpolung) during C-N bond formation relative to traditional approaches. The use of nitroalkanes as acyl anion equivalents provides a conceptually innovative approach to amide and peptide synthesis, and one that might ultimately provide for efficient peptide synthesis that is fully reliant on enantioselective methods. PMID:20577205

Rational approaches for engineering novel functionalities in carbon-carbon bond forming enzymes

PubMed Central

Baker, Perrin; Seah, Stephen Y. K.

2012-01-01

Enzymes that catalyze carbon-carbon bond formation can be exploited as biocatalyst for synthetic organic chemistry. However, natural enzymes frequently do not possess the required properties or specificities to catalyze industrially useful transformations. This mini-review describes recent work using knowledge-guided site-specific mutagenesis of key active site residues to alter substrate specificity, stereospecificity and reaction specificity of these enzymes. In addition, examples of de novo designed enzymes that catalyze C-C bond reactions not found in nature will be discussed. PMID:24688644

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.

Optimizing dentin bond durability: strategies to prevent hydrolytic degradation of the hybrid layer

PubMed Central

Tjäderhane, Leo; Nascimento, Fabio D.; Breschi, Lorenzo; Mazzoni, Annalisa; Tersariol, Ivarne L.S.; Geraldeli, Saulo; Tezvergil-Mutluay, Arzu; Carrilho, Marcela; Carvalho, Ricardo M.; Tay, Franklin R.; Pashley, David H.

2014-01-01

Objectives Endogenous dentin collagenolytic enzymes, matrix metalloproteinases (MMPs) and cysteine cathepsins, are responsible for the time-related hydrolysis of collagen matrix of the hybrid layers. As the integrity of the collagen matrix is essential for the preservation of long-term dentin bond strength, inhibition or inactivation of endogenous dentin proteases is necessary for durable resin-bonded composite resin restorations. Methods Dentin contains collagenolytic enzymes, matrix metalloproteinases (MMPs) and cysteine cathepsins, which are responsible for the hydrolytic degradation of collagen matrix in the bonded interface. Several tentative approaches to prevent enzyme function either directly or indirectly have been proposed in the literature. Results Chlorhexidine, a general inhibitor of both MMPs and cysteine cathepsins, applied before primer/adhesive application is the most tested method. In general, these experiments have shown that enzyme inhibition is a promising scheme to improve hybrid layer preservation and bond strength durability. Other enzyme inhibitors, e.g. enzyme-inhibiting monomers and antimicrobial compounds, may be considered promising alternatives that would allow more simple clinical application than chlorhexidine. Cross-linking collagen and/or dentin organic matrix-bound enzymes could render hybrid layer organic matrix resistant to degradation, and complete removal of water from the hybrid layer with ethanol wet bonding or biomimetic remineralization should eliminate hydrolysis of both collagen and resin components. Significance Identification of the enzymes responsible for the hydrolysis of hybrid layer collagen and understanding their function has prompted several innovative approaches to retain the hybrid layer integrity and strong dentin bonding. The ultimate goal, prevention of collagen matrix degradation with techniques and commercially available materials that are simple and effective in clinical settings may be achievable in several ways, and will likely become reality in the near future. PMID:23953737

Activation of remote meta-C-H bonds assisted by an end-on template.

PubMed

Leow, Dasheng; Li, Gang; Mei, Tian-Sheng; Yu, Jin-Quan

2012-06-27

Functionalization of unactivated carbon-hydrogen (C-H) single bonds is an efficient strategy for rapid generation of complex molecules from simpler ones. However, it is difficult to achieve selectivity when multiple inequivalent C-H bonds are present in the target molecule. The usual approach is to use σ-chelating directing groups, which lead to ortho-selectivity through the formation of a conformationally rigid six- or seven-membered cyclic pre-transition state. Despite the broad utility of this approach, proximity-driven reactivity prevents the activation of remote C-H bonds. Here we report a class of easily removable nitrile-containing templates that direct the activation of distal meta-C-H bonds (more than ten bonds away) of a tethered arene. We attribute this new mode of C-H activation to a weak 'end-on' interaction between the linear nitrile group and the metal centre. The 'end-on' coordination geometry relieves the strain of the cyclophane-like pre-transition state of the meta-C-H activation event. In addition, this template overrides the intrinsic electronic and steric biases as well as ortho-directing effects with two broadly useful classes of arene substrates (toluene derivatives and hydrocinnamic acids).

Remote C-H Activation of Quinolines through Copper-Catalyzed Radical Cross-Coupling.

PubMed

Xu, Jun; Shen, Chao; Zhu, Xiaolei; Zhang, Pengfei; Ajitha, Manjaly J; Huang, Kuo-Wei; An, Zhongfu; Liu, Xiaogang

2016-03-18

Achieving site selectivity in carbon-hydrogen (C-H) functionalization reactions is a formidable challenge in organic chemistry. Herein, we report a novel approach to activating remote C-H bonds at the C5 position of 8-aminoquinoline through copper-catalyzed sulfonylation under mild conditions. Our strategy shows high conversion efficiency, a broad substrate scope, and good toleration with different functional groups. Furthermore, our mechanistic investigations suggest that a single-electron-transfer process plays a vital role in generating sulfonyl radicals and subsequently initiating C-S cross-coupling. Importantly, our copper-catalyzed remote functionalization protocol can be expanded for the construction of a variety of chemical bonds, including C-O, C-Br, C-N, C-C, and C-I. These findings provide a fundamental insight into the activation of remote C-H bonds, while offering new possibilities for rational design of drug molecules and optoelectronic materials requiring specific modification of functional groups. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Remote site-selective C–H activation directed by a catalytic bifunctional template

PubMed Central

Zhang, Zhipeng; Tanaka, Keita; Yu, Jin-Quan

2017-01-01

Converting C–H bonds directly into carbon-carbon and carbon-heteroatom bonds can significantly improve step-economy in synthesis by providing alternative disconnections to traditional functional group manipulations. In this context, directed C–H activation reactions have been extensively explored for regioselective functionalization1-5. Though applicability can be severely curtailed by distance from the directing group and the shape of the molecule, a number of approaches have been developed to overcome this limitation6-12. For instance, recognition of the distal and geometric relationship between an existing functional group and multiple C–H bonds has recently been exploited to achieve meta-selective C–H activation by use of a covalently attached U-shaped template13-17. However, stoichiometric installation of the template is not feasible in the absence of an appropriate functional group handle. Here we report the design of a catalytic, bifunctional template that binds heterocyclic substrate via reversible coordination instead of covalent linkage, allowing remote site-selective C–H olefination of heterocycles. The two metal centers coordinated to this template play different roles; anchoring substrates to the proximity of catalyst and cleaving the remote C–H bonds respectively. Using this strategy, we demonstrate remote site-selective C–H olefination of heterocyclic substrates which do not have functional group handles for covalently attaching templates. PMID:28273068

Effective scheme for partitioning covalent bonds in density-functional embedding theory: From molecules to extended covalent systems.

PubMed

Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele

2016-12-28

Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit

NASA Astrophysics Data System (ADS)

Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

2007-11-01

The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Møller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: benchmarks approaching the complete basis set limit.

PubMed

Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

2007-11-14

The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Moller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

Exact exchange and Wilson-Levy correlation: a pragmatic device for studying complex weakly-bonded systems.

PubMed

Walsh, T R

2005-02-07

The Wilson-Levy (WL) correlation functional is used together with Hartree-Fock (HF) theory to evaluate interaction energies at intermediate separations (i.e. around equilibrium separation) for several weakly-bonded systems. The HF+WL approach reproduces binding trends for all complexes studied: selected rare-gas dimers, isomers of the methane dimer, benzene dimer and naphthalene dimer, and base-pair stacking structures for pyrimidine, cytosine, uracil and guanine dimers. These HF+WL data are contrasted against results obtained from some popular functionals (including B3LYP and PBE), as well as two newly-developed functionals, X3LYP and xPBE. The utility of HF+WL, with reference to exact-exchange (EXX) density-functional theory, is discussed in terms of a suggested EXXWL exchange-correlation functional.

Ab initio study on the structural and electronic properties of water surrounding a multifunctional nanoprobe

NASA Astrophysics Data System (ADS)

Xia, Xiuli; Shao, Yuanzhi

2018-02-01

We report the magneto-electric behavior of a dual-modality biomedical nanoprobe, a ternary nanosystem consisting of gold and gadolinia clusters and water molecules, with the effect of both nanoclusters on the structural and electronic properties of water. The hydrogen-oxygen bond lengths and angles as well as electronic charges of water molecules surrounding both nanoclusters were calculated using Hubbard U corrected density functional theory aided by molecular dynamics approach. The calculations reveal existence of a magneto-electric interaction between gold and gadolinium oxide nanoclusters, which influences the physical properties of surrounding water remarkably. A broader (narrower) distribution of Hsbnd O bond lengths (Hsbnd Osbnd H bond angles) was observed at the presence of either gold or gadolinia nanoclusters. The presence of Gd6O9 cluster leads to the larger charges of neighbour oxygen atoms. The distribution of oxygen atom charges becomes border when both Gd6O9 and Au13 clusters coexist. Ab initio calculation provides a feasible approach to explore the most essential interactions among functional components of a multimodal nanoprobe applied in aqueous environment.

Late Stage Azidation of Complex Molecules

PubMed Central

2016-01-01

Selective functionalization of complex scaffolds is a promising approach to alter the pharmacological profiles of natural products and their derivatives. We report the site-selective azidation of benzylic and aliphatic C–H bonds in complex molecules catalyzed by the combination of Fe(OAc)2 and a PyBox ligand. The same system also catalyzes the trifluoromethyl azidation of olefins to form derivatives of natural products containing both fluorine atoms and azides. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Azides obtained by functionalization of C–H and C=C bonds were converted to the corresponding amines, amides, and triazoles, thus providing a wide variety of nitrogen-containing complex molecules. PMID:27800554

New Approaches to Waterproofing of Space Shuttle Insulating Materials

NASA Technical Reports Server (NTRS)

Blum, Yigal D.; Johnson, Sylvia M.; Chen, Paul

1997-01-01

Future reusable space vehicles will be in service much more frequently than current space shuttles. Therefore, rapid reconditioning of spacecraft will be required. Currently, the waterproofing of space shuttles after each re-entry takes 72 hours and requires substantial labor. In addition, the currently used waterproofing reagent, DiMethylEthoxySilane (DMES), is considered toxic, and ethanol fumes are released during its hydrolytic activation. Consequently, a long time period, which is not acceptable for future operations, is needed to ensure that 0 the excess volatile compounds are removed before further maintenance of the space vehicle can be performed. The objective of this project was to assist NASA Ames in finding improved waterproofing systems by identifying suitable waterproofing agents that can be applied by vapor phase deposition and will be less toxic, bond more rapidly to the insulation material surface, and potentially have higher thermal stability than the DMES system. Several approaches to achieve faster waterproofing with less toxicity were assessed using the following alternatives: Reactive volatile compounds that are rapidly deposited by chemical bonding at the surface and leave no toxic volatiles. Reactive reagents that are the least toxic. Nonvolatile reagents that are very reactive and bond strongly to the insulating material surface. Three specific types of potential reagents were chosen for evaluation in this project: 1. Volatile reagents with Si-Cl functional groups for vapor deposition 2. Volatile reagents with Si-H functional groups for vapor deposition 3. Nonvolatile oligomeric or polymeric reactive siloxanes that are assumed to have higher thermal stability and/or strong bonding to the insulating material. The chemistry involved in the project was targeted at the generation of intermediates having reactive Si-OH bonds for the formation of either volatile species or polymeric species that bond rapidly to the surface and also cure rapidly. We focused on two chemical reactions@-hydrolysis of Si-Cl bonds and catalytic dehydrocoupling of Si-H bonds.

Surface-Initiated Polymerization with Poly(n-hexylisocyanate) to Covalently Functionalize Silica Nanoparticles.

PubMed

Vatansever, Fatma; Hamblin, Michael R

2017-02-01

New methods are needed for covalent functionalization of nanoparticles-surface with organic polymer coronas to generate polymeric nanocomposite in a controlled manner. Here we report the use of a surface-initiated polymerization approach, mediated by titanium (IV) catalysis, to grow poly( n -hexylisocyanate) chains from silica surface. Two pathways were used to generate the interfacing in these nano-hybrids. In the first one, the nanoparticles was "seeded" with SiCl4, followed by reaction with 1,6-hexanediol to form hydroxyl groups attached directly to the surface via O-Si-O bonding. In the second pathway, the nanoparticles were initially exposed to a 9:1 mixture of trimethyl silyl chloride and chlorodimethyl octenyl silane which was then followed by hydroboration of the double bonds, to afford hydroxyl groups with a spatially controlled density and surface-attachment via O-Si-C bonding. These functionalized surfaces were then activated with the titanium tetrachloride catalyst. In our approach, thus surface tethered catalyst provided the sites for n -hexyl isocyanate monomer insertion, to "build up" the surface-grown polymer layers from the "bottom-up". A final end-capping, to seal off the chain ends, was done via acetyl chloride. Compounds were characterized by FT-IR, 1H-NMR, GC-MS, GPC, and thermogravimetric analyses.

Surface-Initiated Polymerization with Poly(n-hexylisocyanate) to Covalently Functionalize Silica Nanoparticles

PubMed Central

Vatansever, Fatma; Hamblin, Michael R.

2017-01-01

New methods are needed for covalent functionalization of nanoparticles-surface with organic polymer coronas to generate polymeric nanocomposite in a controlled manner. Here we report the use of a surface-initiated polymerization approach, mediated by titanium (IV) catalysis, to grow poly(n-hexylisocyanate) chains from silica surface. Two pathways were used to generate the interfacing in these nano-hybrids. In the first one, the nanoparticles was “seeded” with SiCl4, followed by reaction with 1,6-hexanediol to form hydroxyl groups attached directly to the surface via O-Si-O bonding. In the second pathway, the nanoparticles were initially exposed to a 9:1 mixture of trimethyl silyl chloride and chlorodimethyl octenyl silane which was then followed by hydroboration of the double bonds, to afford hydroxyl groups with a spatially controlled density and surface-attachment via O-Si-C bonding. These functionalized surfaces were then activated with the titanium tetrachloride catalyst. In our approach, thus surface tethered catalyst provided the sites for n-hexyl isocyanate monomer insertion, to “build up” the surface-grown polymer layers from the “bottom-up”. A final end-capping, to seal off the chain ends, was done via acetyl chloride. Compounds were characterized by FT-IR, 1H-NMR, GC-MS, GPC, and thermogravimetric analyses. PMID:28989336

Bonding in phase change materials: concepts and misconceptions.

PubMed

Jones, R O

2018-04-18

Bonding concepts originating in chemistry are surveyed from a condensed matter perspective, beginning around 1850 with 'valence' and the word 'bond' itself. The analysis of chemical data in the 19th century resulted in astonishing progress in understanding the connectivity and stereochemistry of molecules, almost without input from physicists until the development of quantum mechanics in 1925 and afterwards. The valence bond method popularized by Pauling and the molecular orbital methods of Hund, Mulliken, Bloch, and Hückel play major roles in the subsequent development, as does the central part played by the kinetic energy in covalent bonding (Ruedenberg and others). 'Metallic' (free electron) and related approaches, including pseudopotential and density functional theories, have been remarkably successful in understanding structures and bonding in molecules and solids. We discuss these concepts in the context of phase change materials, which involve the rapid and reversible transition between amorphous and crystalline states, and note the confusion that some have caused, in particular 'resonance' and 'resonant bonding'.

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Makowski, Mariusz; Augustynowicz, Antoni; Liwo, Adam

2017-03-01

A general and systematic method for the derivation of the functional expressions for the effective energy terms in coarse-grained force fields of polymer chains is proposed. The method is based on the expansion of the potential of mean force of the system studied in the cluster-cumulant series and expanding the all-atom energy in the Taylor series in the squares of interatomic distances about the squares of the distances between coarse-grained centers, to obtain approximate analytical expressions for the cluster cumulants. The primary degrees of freedom to average about are the angles for collective rotation of the atoms contained in the coarse-grained interaction sites about the respective virtual-bond axes. The approach has been applied to the revision of the virtual-bond-angle, virtual-bond-torsional, and backbone-local-and-electrostatic correlation potentials for the UNited RESidue (UNRES) model of polypeptide chains, demonstrating the strong dependence of the torsional and correlation potentials on virtual-bond angles, not considered in the current UNRES. The theoretical considerations are illustrated with the potentials calculated from the ab initio potential-energy surface of terminally blocked alanine by numerical integration and with the statistical potentials derived from known protein structures. The revised torsional potentials correctly indicate that virtual-bond angles close to 90° result in the preference for the turn and helical structures, while large virtual-bond angles result in the preference for polyproline II and extended backbone geometry. The revised correlation potentials correctly reproduce the preference for the formation of β-sheet structures for large values of virtual-bond angles and for the formation of α-helical structures for virtual-bond angles close to 90°.

Systematic approach to developing empirical interatomic potentials for III-N semiconductors

NASA Astrophysics Data System (ADS)

Ito, Tomonori; Akiyama, Toru; Nakamura, Kohji

2016-05-01

A systematic approach to the derivation of empirical interatomic potentials is developed for III-N semiconductors with the aid of ab initio calculations. The parameter values of empirical potential based on bond order potential are determined by reproducing the cohesive energy differences among 3-fold coordinated hexagonal, 4-fold coordinated zinc blende, wurtzite, and 6-fold coordinated rocksalt structures in BN, AlN, GaN, and InN. The bond order p is successfully introduced as a function of the coordination number Z in the form of p = a exp(-bZn ) if Z ≤ 4 and p = (4/Z)α if Z ≥ 4 in empirical interatomic potential. Moreover, the energy difference between wurtzite and zinc blende structures can be successfully evaluated by considering interaction beyond the second-nearest neighbors as a function of ionicity. This approach is feasible for developing empirical interatomic potentials applicable to a system consisting of poorly coordinated atoms at surfaces and interfaces including nanostructures.

Curli mediate bacterial adhesion to fibronectin via tensile multiple bonds

NASA Astrophysics Data System (ADS)

Oh, Yoo Jin; Hubauer-Brenner, Michael; Gruber, Hermann J.; Cui, Yidan; Traxler, Lukas; Siligan, Christine; Park, Sungsu; Hinterdorfer, Peter

2016-09-01

Many enteric bacteria including pathogenic Escherichia coli and Salmonella strains produce curli fibers that bind to host surfaces, leading to bacterial internalization into host cells. By using a nanomechanical force-sensing approach, we obtained real-time information about the distribution of molecular bonds involved in the adhesion of curliated bacteria to fibronectin. We found that curliated E. coli and fibronectin formed dense quantized and multiple specific bonds with high tensile strength, resulting in tight bacterial binding. Nanomechanical recognition measurements revealed that approximately 10 bonds were disrupted either sequentially or simultaneously under force load. Thus the curli formation of bacterial surfaces leads to multi-bond structural components of fibrous nature, which may explain the strong mechanical binding of curliated bacteria to host cells and unveil the functions of these proteins in bacterial internalization and invasion.

Catalytic activation of carbon-carbon bonds in cyclopentanones.

PubMed

Xia, Ying; Lu, Gang; Liu, Peng; Dong, Guangbin

2016-11-24

In the chemical industry, molecules of interest are based primarily on carbon skeletons. When synthesizing such molecules, the activation of carbon-carbon single bonds (C-C bonds) in simple substrates is strategically important: it offers a way of disconnecting such inert bonds, forming more active linkages (for example, between carbon and a transition metal) and eventually producing more versatile scaffolds. The challenge in achieving such activation is the kinetic inertness of C-C bonds and the relative weakness of newly formed carbon-metal bonds. The most common tactic starts with a three- or four-membered carbon-ring system, in which strain release provides a crucial thermodynamic driving force. However, broadly useful methods that are based on catalytic activation of unstrained C-C bonds have proven elusive, because the cleavage process is much less energetically favourable. Here we report a general approach to the catalytic activation of C-C bonds in simple cyclopentanones and some cyclohexanones. The key to our success is the combination of a rhodium pre-catalyst, an N-heterocyclic carbene ligand and an amino-pyridine co-catalyst. When an aryl group is present in the C3 position of cyclopentanone, the less strained C-C bond can be activated; this is followed by activation of a carbon-hydrogen bond in the aryl group, leading to efficient synthesis of functionalized α-tetralones-a common structural motif and versatile building block in organic synthesis. Furthermore, this method can substantially enhance the efficiency of the enantioselective synthesis of some natural products of terpenoids. Density functional theory calculations reveal a mechanism involving an intriguing rhodium-bridged bicyclic intermediate.

Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and -Stacking

DOE PAGES

Shewmon, Nathan; Watkins, Davita; Galindo, Johan; ...

2015-07-20

For organic photovoltaic (OPV) cells based on the bulk heterojunction (BHJ) structure, it remains challenging to rationally control the degree of phase separation and percolation within blends of donors and acceptors to secure optimal charge separation and transport. Reported is a bottom-up, supramolecular approach to BHJ OPVs wherein tailored hydrogen bonding (H-bonding) interactions between π-conjugated electron donor molecules encourage formation of vertically aligned donor π-stacks while simultaneously suppressing lateral aggregation; the programmed arrangement facilitates fine mixing with fullerene acceptors and efficient charge transport. The approach is illustrated using conventional linear or branched quaterthiophene donor chromophores outfitted with terminal functional groupsmore » that are either capable or incapable of self-complementary H-bonding. When applied to OPVs, the H-bond capable donors yield a twofold enhancement in power conversion efficiency relative to the comparator systems, with a maximum external quantum efficiency of 64%. H-bond promoted assembly results in redshifted absorption (in neat films and donor:C 60 blends) and enhanced charge collection efficiency despite disparate donor chromophore structure. Both features positively impact photocurrent and fill factor in OPV devices. Film structural characterization by atomic force microscopy, transmission electron microscopy, and grazing incidence wide angle X-ray scattering reveals a synergistic interplay of lateral H-bonding interactions and vertical π-stacking for directing the favorable morphology of the BHJ.« less

Weak Coordination as a Powerful Means for Developing Broadly Useful C–H Functionalization Reactions

PubMed Central

Engle, Keary M.; Mei, Tian-Sheng; Wasa, Masayuki

2011-01-01

Conspectus Reactions that convert carbon–hydrogen (C–H) bonds into carbon–carbon (C–C) or carbon–heteroatom (C–Y) bonds are attractive tools for organic chemists, potentially expediting the synthesis of target molecules through new disconnections in retrosynthetic analysis. Despite extensive inorganic and organometallic study of the insertion of homogeneous metal species into unactivated C–H bonds, practical applications of this technology in organic chemistry are still rare. Only in the past decade have metal-catalyzed C–H functionalization reactions become more widely utilized in organic synthesis. Research in the area of homogeneous transition metal–catalyzed C–H functionalization can be broadly grouped into two subfields. They reflect different approaches and goals and thus have different challenges and opportunities. One approach involves reactions of completely unfunctionalized aromatic and aliphatic hydrocarbons, which we refer to as “first functionalization.” Here the substrates are nonpolar and hydrophobic and thus interact very weakly with polar metal species. To overcome this weak affinity and drive metal-mediated C–H cleavage, chemists often use hydrocarbon substrates in large excess (for example, as solvent). Because highly reactive metal species are needed in first functionalization, controlling the chemoselectivity to avoid over-functionalization is often difficult. Additionally, because both substrates and products are comparatively low-value chemicals, developing cost-effective catalysts with exceptionally high turnover numbers that are competitive with alternatives (including heterogeneous catalysts) is challenging. Although an exciting field, first functionalization is beyond the scope of this Account. The second subfield of C–H functionalization involves substrates containing one or more pre-existing functional groups, termed “further functionalization.” One advantage of this approach is that the existing functional group (or groups) can be used to chelate the metal catalyst and position it for selective C–H cleavage. Precoordination can overcome the paraffin nature of C–H bonds by increasing the effective concentration of the substrate so that it needn't be used as solvent. From a synthetic perspective, it is desirable to use a functional group that is an intrinsic part of the substrate so that extra steps for installation and removal of an external directing group can be avoided. In this way, dramatic increases in molecular complexity can be accomplished in a single stroke through stereo- and site-selective introduction of a new functional group. Although reactivity is a major challenge (as with first functionalization), the philosophy in further functionalization differs—the major challenge is developing reactions that work with predictable selectivity in intricately functionalized contexts on commonly occurring structural motifs. In this Account, we focus on an emergent theme within the further functionalization literature: the use of commonly occurring functional groups to direct C–H cleavage through weak coordinations. We discuss our motivation for studying Pd-catalyzed C–H functionalization assisted by weakly coordinating functional groups and chronicle our endeavors to bring reactions of this type to fruition. Through this approach, we have developed reactions with a diverse range of substrates and coupling partners, with the broad scope likely stemming from higher reactivity of the less stable cyclopalladated intermediates held in place by weak coordinations. PMID:22166158

Weak coordination as a powerful means for developing broadly useful C-H functionalization reactions.

PubMed

Engle, Keary M; Mei, Tian-Sheng; Wasa, Masayuki; Yu, Jin-Quan

2012-06-19

Reactions that convert carbon-hydrogen (C-H) bonds into carbon-carbon (C-C) or carbon-heteroatom (C-Y) bonds are attractive tools for organic chemists, potentially expediting the synthesis of target molecules through new disconnections in retrosynthetic analysis. Despite extensive inorganic and organometallic study of the insertion of homogeneous metal species into unactivated C-H bonds, practical applications of this technology in organic chemistry are still rare. Only in the past decade have metal-catalyzed C-H functionalization reactions become more widely utilized in organic synthesis. Research in the area of homogeneous transition metal-catalyzed C-H functionalization can be broadly grouped into two subfields. They reflect different approaches and goals and thus have different challenges and opportunities. One approach involves reactions of completely unfunctionalized aromatic and aliphatic hydrocarbons, which we refer to as "first functionalization". Here the substrates are nonpolar and hydrophobic and thus interact very weakly with polar metal species. To overcome this weak affinity and drive metal-mediated C-H cleavage, chemists often use hydrocarbon substrates in large excess (for example, as solvent). Because highly reactive metal species are needed in first functionalization, controlling the chemoselectivity to avoid overfunctionalization is often difficult. Additionally, because both substrates and products are comparatively low-value chemicals, developing cost-effective catalysts with exceptionally high turnover numbers that are competitive with alternatives (including heterogeneous catalysts) is challenging. Although an exciting field, first functionalization is beyond the scope of this Account. The second subfield of C-H functionalization involves substrates containing one or more pre-existing functional groups, termed "further functionalization". One advantage of this approach is that the existing functional group (or groups) can be used to chelate the metal catalyst and position it for selective C-H cleavage. Precoordination can overcome the paraffin nature of C-H bonds by increasing the effective concentration of the substrate so that it need not be used as solvent. From a synthetic perspective, it is desirable to use a functional group that is an intrinsic part of the substrate so that extra steps for installation and removal of an external directing group can be avoided. In this way, dramatic increases in molecular complexity can be accomplished in a single stroke through stereo- and site-selective introduction of a new functional group. Although reactivity is a major challenge (as with first functionalization), the philosophy in further functionalization differs; the major challenge is developing reactions that work with predictable selectivity in intricately functionalized contexts on commonly occurring structural motifs. In this Account, we focus on an emergent theme within the further functionalization literature: the use of commonly occurring functional groups to direct C-H cleavage through weak coordination. We discuss our motivation for studying Pd-catalyzed C-H functionalization assisted by weakly coordinating functional groups and chronicle our endeavors to bring reactions of this type to fruition. Through this approach, we have developed reactions with a diverse range of substrates and coupling partners, with the broad scope likely stemming from the high reactivity of the cyclopalladated intermediates, which are held together through weak interactions.

Application of Time-Dependent Density Functional and Natural Bond Orbital Theories to the UV-vis Absorption Spectra of Some Phenolic Compounds.

PubMed

Marković, Svetlana; Tošović, Jelena

2015-09-03

The UV-vis properties of 22 natural phenolic compounds, comprising anthraquinones, neoflavonoids, and flavonoids were systematically examined. The time-dependent density functional theory (TDDFT) approach in combination with the B3LYP, B3LYP-D2, B3P86, and M06-2X functionals was used to simulate the UV-vis spectra of the investigated compounds. It was shown that all methods exhibit very good (B3LYP slightly better) performance in reproducing the examined UV-vis spectra. However, the shapes of the Kohn-Sham molecular orbitals (MOs) involved in electronic transitions were misleading in constructing the MO correlation diagrams. To provide better understanding of redistribution of electron density upon excitation, the natural bond orbital (NBO) analysis was applied. Bearing in mind the spatial and energetic separations, as well as the character of the π bonding, lone pair, and π* antibonding natural localized molecular orbitals (NLMOs), the "NLMO clusters" were constructed. NLMO cluster should be understood as a part of a molecule characterized with distinguished electron density. It was shown that all absorption bands including all electronic transitions need to be inspected to fully understand the UV-vis spectrum of a certain compound, and, thus, to learn more about its UV-vis light absorption. Our investigation showed that the TDDFT and NBO theories are complementary, as the results from the two approaches can be combined to interpret the UV-vis spectra. Agreement between the predictions of the TDDFT approach and those based on the NLMO clusters is excellent in the case of major electronic transitions and long wavelengths. It should be emphasized that the approach for investigation of UV-vis light absorption based on the NLMO clusters is applied for the first time.

Characterizing Bonding Patterns in Diradicals and Triradicals by Density-Based Wave Function Analysis: A Uniform Approach.

PubMed

Orms, Natalie; Rehn, Dirk R; Dreuw, Andreas; Krylov, Anna I

2018-02-13

Density-based wave function analysis enables unambiguous comparisons of the electronic structure computed by different methods and removes ambiguity of orbital choices. We use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high- and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such as polyradicals. We show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of the bonding pattern.

Application of Density Functional Theory to Systems Containing Metal Atoms

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

2006-01-01

The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+n, MNO+, and MCO+2. The DFT works well for frequencies and geometries, even in case with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of successes as well as failures of DFT will be given.

Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

NASA Astrophysics Data System (ADS)

Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

2015-03-01

We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

Copper-Catalyzed Domino Three-Component Approach for the Assembly of 2-Aminated Benzimidazoles and Quinazolines.

PubMed

Tran, Lam Quang; Li, Jihui; Neuville, Luc

2015-06-19

A copper-promoted three-component synthesis of 2-aminobenzimidazoles (1) or of 2-aminoquinazolines (2) involving cyanamides, arylboronic acids, and amines has been developed. The operationally simple oxidative process, performed in the presence of K2CO3, a catalytic amount of CuCl2·2H2O, 2,2'-bipyridine, and an O2 atmosphere (1 atm), allows the rapid assembly of either benzimidazoles or quinazolines starting from aryl- or benzyl-substituted cyanamides, respectively. In this process, the copper promotes the formation of three bonds, two C-N bonds, and an additional bond resulting from C-H functionalization event.

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.

QSPR analysis of the partitioning of vaporous chemicals in a water-gas phase system and the water solubility of liquid and solid chemicals on the basis of fragment and physicochemical similarity and hybot descriptors.

PubMed

Raevsky, O; Andreeva, E; Raevskaja, O; Skvortsov, V; Schaper, K

2005-01-01

QSPR analyses of the solubility in water of 558 vapors, 786 liquids and 2045 solid organic neutral chemicals and drugs are presented. Simultaneous consideration of H-bond acceptor and donor factors leads to a good description of the solubility of vapors and liquids. A volume-related term was found to have an essential negative contribution to the solubility of liquids. Consideration of polarizability, H-bond acceptor and donor factors and indicators for a few functional groups, as well as the experimental solubility values of structurally nearest neighbors yielded good correlations for liquids. The application of Yalkowsky's "General Solubility Equation" to 1063 solid chemicals and drugs resulted in a correlation of experimental vs calculated log S values with only modest statistical criteria. Two approaches to derive predictive models for solubility of solid chemicals and drugs were tested. The first approach was based on the QSPR for liquids together with indicator variables for different functional groups. Furthermore, a calculation of enthalpies for intermolecular complexes in crystal lattices, based on new H-bond potentials, was carried out for the better consideration of essential solubility- decreasing effects in the solid state, as compared with the liquid state. The second approach was based on a combination of similarity considerations and traditional QSPR. Both approaches lead to high quality predictions with average absolute errors on the level of experimental log S determination.

Efficient Transition State Optimization of Periodic Structures through Automated Relaxed Potential Energy Surface Scans.

PubMed

Plessow, Philipp N

2018-02-13

This work explores how constrained linear combinations of bond lengths can be used to optimize transition states in periodic structures. Scanning of constrained coordinates is a standard approach for molecular codes with localized basis functions, where a full set of internal coordinates is used for optimization. Common plane wave-codes for periodic boundary conditions almost exlusively rely on Cartesian coordinates. An implementation of constrained linear combinations of bond lengths with Cartesian coordinates is described. Along with an optimization of the value of the constrained coordinate toward the transition states, this allows transition optimization within a single calculation. The approach is suitable for transition states that can be well described in terms of broken and formed bonds. In particular, the implementation is shown to be effective and efficient in the optimization of transition states in zeolite-catalyzed reactions, which have high relevance in industrial processes.

Theoretical modeling of infrared spectra of the hydrogen and deuterium bond in aspirin crystal

NASA Astrophysics Data System (ADS)

Ghalla, Houcine; Rekik, Najeh; Michta, Anna; Oujia, Brahim; Flakus, Henryk T.

2010-01-01

An extended quantum theoretical approach of the ν IR lineshape of cyclic dimers of weakly H-bonded species is proposed. We have extended a previous approach [M.E.-A. Benmalti, P. Blaise, H.T. Flakus, O. Henri-Rousseau, Chem. Phys. 320 (2006) 267] by accounting for the anharmonicity of the slow mode which is described by a "Morse" potential in order to reproduce the polarized infrared spectra of the hydrogen and deuterium bond in acetylsalicylic acid (aspirin) crystals. From comparison of polarized IR spectra of isotopically neat and isotopically diluted aspirin crystals it resulted that centrosymmetric aspirin dimer was the bearer of the crystal main spectral properties. In this approach, the adiabatic approximation is performed for each separate H-bond bridge of the dimer and a strong non-adiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Within the strong anharmonic coupling theory, according to which the X-H→⋯Y high-frequency mode is anharmonically coupled to the H-bond bridge, this model incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the anharmonicity for the H-bond bridge. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The evaluated spectra are in fairly good agreement with the experimental ones by using a minimum number of independent parameters. The effect of deuteration has been well reproduced by reducing simply the angular frequency of the fast mode and the anharmonic coupling parameter.

Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach.

PubMed

Bellucci, Michael A; Coker, David F

2011-07-28

We describe a new method for constructing empirical valence bond potential energy surfaces using a parallel multilevel genetic program (PMLGP). Genetic programs can be used to perform an efficient search through function space and parameter space to find the best functions and sets of parameters that fit energies obtained by ab initio electronic structure calculations. Building on the traditional genetic program approach, the PMLGP utilizes a hierarchy of genetic programming on two different levels. The lower level genetic programs are used to optimize coevolving populations in parallel while the higher level genetic program (HLGP) is used to optimize the genetic operator probabilities of the lower level genetic programs. The HLGP allows the algorithm to dynamically learn the mutation or combination of mutations that most effectively increase the fitness of the populations, causing a significant increase in the algorithm's accuracy and efficiency. The algorithm's accuracy and efficiency is tested against a standard parallel genetic program with a variety of one-dimensional test cases. Subsequently, the PMLGP is utilized to obtain an accurate empirical valence bond model for proton transfer in 3-hydroxy-gamma-pyrone in gas phase and protic solvent. © 2011 American Institute of Physics

Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

DOE PAGES

Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

2015-06-04

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

Statistical mechanics of high-density bond percolation

NASA Astrophysics Data System (ADS)

Timonin, P. N.

2018-05-01

High-density (HD) percolation describes the percolation of specific κ -clusters, which are the compact sets of sites each connected to κ nearest filled sites at least. It takes place in the classical patterns of independently distributed sites or bonds in which the ordinary percolation transition also exists. Hence, the study of series of κ -type HD percolations amounts to the description of classical clusters' structure for which κ -clusters constitute κ -cores nested one into another. Such data are needed for description of a number of physical, biological, and information properties of complex systems on random lattices, graphs, and networks. They range from magnetic properties of semiconductor alloys to anomalies in supercooled water and clustering in biological and social networks. Here we present the statistical mechanics approach to study HD bond percolation on an arbitrary graph. It is shown that the generating function for κ -clusters' size distribution can be obtained from the partition function of the specific q -state Potts-Ising model in the q →1 limit. Using this approach we find exact κ -clusters' size distributions for the Bethe lattice and Erdos-Renyi graph. The application of the method to Euclidean lattices is also discussed.

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

PubMed Central

2015-01-01

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

Microsolvation of the 5-hydroxyindole cation (5HI+) with nonpolar and quadrupolar ligands: Infrared photodissociation spectra of 5HI+-Ln clusters with L = Ar and N2 (n ≤ 3)

NASA Astrophysics Data System (ADS)

Klyne, Johanna; Dopfer, Otto

2017-07-01

Solvation of biomolecules and their building blocks has a strong influence on their structure and function. Herein we characterize the initial microsolvation of the 5-hydroxyindole cation (5HI+) in its 2A″ ground electronic state with nonpolar and quadrupolar ligands (L = Ar, N2) by infrared photodissociation (IRPD) spectroscopy of cold and mass-selected 5HI+-Ln (n ≤ 3) clusters in a molecular beam and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). The isomer-selective OH and NH stretch frequency shifts (ΔνOH/NH) disentangle the competition between H-bonding to the acidic OH and NH groups and π-stacking to the conjugated bicyclic aromatic π-electron system, the intermolecular interaction strengths, and the cluster growth sequence. For 5HI+-Arn, H-bonding and π-stacking strongly compete, indicating that dispersion forces are important for the interaction of 5HI+ with nonpolar ligands. In contrast, for 5HI+-(N2)n clusters, the H-bonds are much stronger than the π-bonds and largely determine the initial solvation process. In all clusters, the OH…L bonds are stronger than the NH…L bonds followed by the π-bonds. The interaction of 5HI+ with N2 is roughly twice stronger than with Ar, mainly due to the additional quadrupole moment of N2. The nature and strength of the individual interactions are quantified by the noncovalent interaction approach. Comparison of 5HI+-L with the corresponding neutral clusters reveals the strong impact of ionization on the total and relative interaction strengths of the H-bonds and π-bonds. In addition, comparison of 5HI+-L with corresponding clusters of the phenol, indole, and pyrrole radical cations illustrates the effects of substitution of functional groups and the addition of aromatic rings to the various subunits of 5HI on the intermolecular potential.

Ab Initio Study of Polarizabilities of Oligothiophene, Oligocyclopentadiene and Oligofulvene and their Cyano Substituted Oligomers

NASA Astrophysics Data System (ADS)

Lagowski, Jolanta; Ferdous, Sultana

2005-03-01

Ab Initio polarizabilities of thiophene, fulvene and cyclopentadiene based conducting oligomers and polymers and their cyano derivatives have been calculated using the Hartree-Fock (HF), configuration interaction (singles) (CIS ) and density functional (DF) theories with 3-21G* basis using Gaussian software. The main motivation of this investigation is to determine the correlation between the excitation energies and polarizabilities for the conjugated systems studied. It has been found that HF and DF approaches give similar magnitudes for polarizabilities whereas CIS theory provides results that are considerably different. All three methods predict similar trends in polarizabilities as a function of oligomer length and bond alternation along the backbone of the oligomers. It has also been observed that the end groups and the number of `double' bonds have a significant effect on the magnitude of polarizability per C-C bond. Comparison with experimental results will be made where possible.

Catalytic activation of carbon–carbon bonds in cyclopentanones

PubMed Central

Xia, Ying; Lu, Gang; Liu, Peng; Dong, Guangbin

2017-01-01

In the chemical industry, molecules of interest are based primarily on carbon skeletons. When synthesizing such molecules, the activation of carbon–carbon single bonds (C–C bonds) in simple substrates is strategically important: it offers a way of disconnecting such inert bonds, forming more active linkages (for example, between carbon and a transition metal) and eventually producing more versatile scaffolds1–13. The challenge in achieving such activation is the kinetic inertness of C–C bonds and the relative weakness of newly formed carbon–metal bonds6,14. The most common tactic starts with a three- or four-membered carbon-ring system9–13, in which strain release provides a crucial thermodynamic driving force. However, broadly useful methods that are based on catalytic activation of unstrained C–C bonds have proven elusive, because the cleavage process is much less energetically favourable. Here we report a general approach to the catalytic activation of C–C bonds in simple cyclopentanones and some cyclohexanones. The key to our success is the combination of a rhodium pre-catalyst, an N-heterocyclic carbene ligand and an amino-pyridine co-catalyst. When an aryl group is present in the C3 position of cyclopentanone, the less strained C–C bond can be activated; this is followed by activation of a carbon–hydrogen bond in the aryl group, leading to efficient synthesis of functionalized α-tetralones—a common structural motif and versatile building block in organic synthesis. Furthermore, this method can substantially enhance the efficiency of the enantioselective synthesis of some natural products of terpenoids. Density functional theory calculations reveal a mechanism involving an intriguing rhodium-bridged bicyclic intermediate. PMID:27806379

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.

Generic approach to access barriers in dehydrogenation reactions

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

Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

Generic approach to access barriers in dehydrogenation reactions

DOE PAGES

Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

2018-03-08

The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

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.

IMPROVED BONDING METHOD

DOEpatents

Padgett, E.V. Jr.; Warf, D.H.

1964-04-28

An improved process of bonding aluminum to aluminum without fusion by ultrasonic vibrations plus pressure is described. The surfaces to be bonded are coated with an aqueous solution of alkali metal stearate prior to assembling for bonding. (AEC) O H19504 Present information is reviewed on steady state proliferation, differentiation, and maturation of blood cells in mammals. Data are cited from metabolic tracer studies, autoradiographic studies, cytologic studies, studies of hematopoietic response to radiation injuries, and computer analyses of blood cell production. A 3-step model for erythropoiesis and a model for granulocyte kinetics are presented. New approaches to the study of lymphocytopoiesis described include extracorporeal blood irradiation to deplete lymphocytic tissue without direct injury to the formative tissues as a means to study the stressed system, function control, and rates of proliferation. It is pointed out that present knowledge indicates that lymphocytes comprise a mixed family, with diverse life spans, functions, and migration patterns with apparent aimless recycling from modes to lymph to blood to nodes that has not yet been quantitated. Areas of future research are postulated. (70 references.) (C.H.)

Global disulfide bond profiling for crude snake venom using dimethyl labeling coupled with mass spectrometry and RADAR algorithm.

PubMed

Huang, Sheng Yu; Chen, Sung Fang; Chen, Chun Hao; Huang, Hsuan Wei; Wu, Wen Guey; Sung, Wang Chou

2014-09-02

Snake venom consists of toxin proteins with multiple disulfide linkages to generate unique structures and biological functions. Determination of these cysteine connections usually requires the purification of each protein followed by structural analysis. In this study, dimethyl labeling coupled with LC-MS/MS and RADAR algorithm was developed to identify the disulfide bonds in crude snake venom. Without any protein separation, the disulfide linkages of several cytotoxins and PLA2 could be solved, including more than 20 disulfide bonds. The results show that this method is capable of analyzing protein mixture. In addition, the approach was also used to compare native cytotoxin 3 (CTX III) and its scrambled isomer, another category of protein mixture, for unknown disulfide bonds. Two disulfide-linked peptides were observed in the native CTX III, and 10 in its scrambled form, X-CTX III. This is the first study that reports a platform for the global cysteine connection analysis on a protein mixture. The proposed method is simple and automatic, offering an efficient tool for structural and functional studies of venom proteins.

The function of duetting in magpie-larks: conflict, cooperation, or commitment?

PubMed

Hall

2000-11-01

Avian duetting is a poorly understood phenomenon despite many hypotheses as to its function. Contrary to the recent view that duetting functions for mate guarding and is a result of conflict between the sexes, Australian magpie-larks, Grallina cyanoleuca, do not use duetting as a paternity guard. I used a playback experiment to investigate the role of antiphonal duetting in territorial defence and pair bond maintenance, two traditional hypotheses about the function of duetting. The experiment showed that, like many nonduetting species, magpie-larks recognize neighbours on the basis of song. It also provided evidence of functional differences between duetting and solo singing which indicate that temporal coordination of song between partners is used to maintain the territory and pair bond. Duets were more threatening territorial signals than solo songs: males initiated more vocalizations in response to playback of duets than playback of solos. Simulated intrusion also caused males and females to approach the speaker together and coordinate more of their vocalizations to form duets. Females did not engage in sex-specific territorial defence, responding equally strongly to playback of male and female song, and maintaining both territory and pair bond by attempting to exclude intruders of either sex. Males initiated more vocalizations in response to playback of male than female song, and their likelihood of duetting appeared to be related more to threats to the pair bond, in particular desertion by their partner. Copyright 2000 The Association for the Study of Animal Behaviour.

Application of Density Functional Theory to Systems Containing Metal Atoms

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

1997-01-01

The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+(sub n), MNO+, and MCO+(sub 2). The DFT works well for frequencies and geometries, even in cases with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of the successes as well as failures of DFT will be given.

Exploring the Interaction Natures in Plutonyl (VI) Complexes with Topological Analyses of Electron Density

PubMed Central

Du, Jiguang; Sun, Xiyuan; Jiang, Gang

2016-01-01

The interaction natures between Pu and different ligands in several plutonyl (VI) complexes are investigated by performing topological analyses of electron density. The geometrical structures in both gaseous and aqueous phases are obtained with B3LYP functional, and are generally in agreement with available theoretical and experimental results when combined with all-electron segmented all-electron relativistic contracted (SARC) basis set. The Pu–Oyl bond orders show significant linear dependence on bond length and the charge of oxygen atoms in plutonyl moiety. The closed-shell interactions were identified for Pu-Ligand bonds in most complexes with quantum theory of atoms in molecules (QTAIM) analyses. Meanwhile, we found that some Pu–Ligand bonds, like Pu–OH−, show weak covalent. The interactive nature of Pu–ligand bonds were revealed based on the interaction quantum atom (IQA) energy decomposition approach, and our results indicate that all Pu–Ligand interactions is dominated by the electrostatic attraction interaction as expected. Meanwhile it is also important to note that the quantum mechanical exchange-correlation contributions can not be ignored. By means of the non-covalent interaction (NCI) approach it has been found that some weak and repulsion interactions existed in plutonyl(VI) complexes, which can not be distinguished by QTAIM, can be successfully identified. PMID:27077844

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.

Characterizing bonding patterns in diradicals and triradicals by density-based wave function analysis: A uniform approach

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

Orms, Natalie; Rehn, Dirk; Dreuw, Andreas

Density-based wave function analysis enables unambiguous comparisons of electronic structure computed by different methods and removes ambiguity of orbital choices. Here, we use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such asmore » polyradicals. We also show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of bonding pattern.« less

Characterizing bonding patterns in diradicals and triradicals by density-based wave function analysis: A uniform approach

DOE PAGES

Orms, Natalie; Rehn, Dirk; Dreuw, Andreas; ...

2017-12-21

Density-based wave function analysis enables unambiguous comparisons of electronic structure computed by different methods and removes ambiguity of orbital choices. Here, we use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such asmore » polyradicals. We also show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of bonding pattern.« less

Ligand-Enabled meta-C–H Activation Using a Transient Mediator

PubMed Central

Wang, Xiao-Chen; Gong, Wei; Fang, Li-Zhen; Zhu, Ru-Yi; Li, Suhua; Engle, Keary M.; Yu, Jin-Quan

2015-01-01

Achieving site selectivity in C–H functionalization reactions is a significant challenge, especially when the target C–H bond is distant from existing functional groups.1–5 Coordination of a functional group to a metal catalyst is often a key driving force and control element in many important reactions including asymmetric hydrogenation,6 epoxidation7, 8, and lithiation9. Exploitation of this effect has led to the development of a broad range of directed C–H activation reactions.10–14 However, such C–H activation methods are limited to proximal C–H bonds, which are spatially and geometrically accessible from the directing functional group. Development of meta-selective C–H functionalizations remains a significant challenge.1–5,15–17 We recently developed a U- shaped template that can be used to overcome this constraint and have shown that it can be used to selectively activate remote meta-C–H bonds.1, 2 While this approach has proven applicable for a diverse set of substrates and catalytic transformations,3–5 the need for a covalently attached complex template is a significant drawback for synthetic applications. In this manuscript, we report an alternative approach, one that employs norbornene as a transient mediator to achieve meta-selective C–H activation with a simple and common ortho-directing group. The use of a newly developed pyridine-based ligand is crucial for relaying the palladium catalyst to the meta position by norbornene following initial ortho- C–H activation. Thus, this catalytic reaction demonstrates the feasibility of switching ortho-selectivity to meta-selectivity in C–H activation of the same substrate by catalyst control. PMID:25754328

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

Bonding in phase change materials: concepts and misconceptions

NASA Astrophysics Data System (ADS)

Jones, R. O.

2018-04-01

Bonding concepts originating in chemistry are surveyed from a condensed matter perspective, beginning around 1850 with ‘valence’ and the word ‘bond’ itself. The analysis of chemical data in the 19th century resulted in astonishing progress in understanding the connectivity and stereochemistry of molecules, almost without input from physicists until the development of quantum mechanics in 1925 and afterwards. The valence bond method popularized by Pauling and the molecular orbital methods of Hund, Mulliken, Bloch, and Hückel play major roles in the subsequent development, as does the central part played by the kinetic energy in covalent bonding (Ruedenberg and others). ‘Metallic’ (free electron) and related approaches, including pseudopotential and density functional theories, have been remarkably successful in understanding structures and bonding in molecules and solids. We discuss these concepts in the context of phase change materials, which involve the rapid and reversible transition between amorphous and crystalline states, and note the confusion that some have caused, in particular ‘resonance’ and ‘resonant bonding’.

Merging allylic carbon-hydrogen and selective carbon-carbon bond activation.

PubMed

Masarwa, Ahmad; Didier, Dorian; Zabrodski, Tamar; Schinkel, Marvin; Ackermann, Lutz; Marek, Ilan

2014-01-09

Since the nineteenth century, many synthetic organic chemists have focused on developing new strategies to regio-, diastereo- and enantioselectively build carbon-carbon and carbon-heteroatom bonds in a predictable and efficient manner. Ideal syntheses should use the least number of synthetic steps, with few or no functional group transformations and by-products, and maximum atom efficiency. One potentially attractive method for the synthesis of molecular skeletons that are difficult to prepare would be through the selective activation of C-H and C-C bonds, instead of the conventional construction of new C-C bonds. Here we present an approach that exploits the multifold reactivity of easily accessible substrates with a single organometallic species to furnish complex molecular scaffolds through the merging of otherwise difficult transformations: allylic C-H and selective C-C bond activations. The resulting bifunctional nucleophilic species, all of which have an all-carbon quaternary stereogenic centre, can then be selectively derivatized by the addition of two different electrophiles to obtain more complex molecular architecture from these easily available starting materials.

Merging allylic carbon-hydrogen and selective carbon-carbon bond activation

NASA Astrophysics Data System (ADS)

Masarwa, Ahmad; Didier, Dorian; Zabrodski, Tamar; Schinkel, Marvin; Ackermann, Lutz; Marek, Ilan

2014-01-01

Since the nineteenth century, many synthetic organic chemists have focused on developing new strategies to regio-, diastereo- and enantioselectively build carbon-carbon and carbon-heteroatom bonds in a predictable and efficient manner. Ideal syntheses should use the least number of synthetic steps, with few or no functional group transformations and by-products, and maximum atom efficiency. One potentially attractive method for the synthesis of molecular skeletons that are difficult to prepare would be through the selective activation of C-H and C-C bonds, instead of the conventional construction of new C-C bonds. Here we present an approach that exploits the multifold reactivity of easily accessible substrates with a single organometallic species to furnish complex molecular scaffolds through the merging of otherwise difficult transformations: allylic C-H and selective C-C bond activations. The resulting bifunctional nucleophilic species, all of which have an all-carbon quaternary stereogenic centre, can then be selectively derivatized by the addition of two different electrophiles to obtain more complex molecular architecture from these easily available starting materials.

Photochemically and Thermally Driven Full-Color Reflection in a Self-Organized Helical Superstructure Enabled by a Halogen-Bonded Chiral Molecular Switch.

PubMed

Wang, Hao; Bisoyi, Hari Krishna; Wang, Ling; Urbas, Augustine M; Bunning, Timothy J; Li, Quan

2018-02-05

Supramolecular approaches toward the fabrication of functional materials and systems have been an enabling endeavor. Recently, halogen bonding has been harnessed as a promising supramolecular tool. Herein we report the synthesis and characterization of a novel halogen-bonded light-driven axially chiral molecular switch. The photoactive halogen-bonded chiral switch is able to induce a self-organized, tunable helical superstructure, that is, cholesteric liquid crystal (CLC), when doped into an achiral liquid crystal (LC) host. The halogen-bonded switch as a chiral dopant has a high helical twisting power (HTP) and shows a large change of its HTP upon photoisomerization. This light-driven dynamic modulation enables reversible selective reflection color tuning across the entire visible spectrum. The chiral switch also displays a temperature-dependent HTP change that enables thermally driven red, green, and blue (RGB) reflection colors in the self-organized helical superstructure. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electronic Structure and Bonding in Complex Biomolecule

NASA Astrophysics Data System (ADS)

Ouyang, Lizhi

2005-03-01

For over a century vitamin B12 and its enzyme cofactor derivates have persistently attracted research efforts for their vital biological role, unique Co-C bonding, rich red-ox chemistry, and recently their candidacies as drug delivery vehicles etc. However, our understanding of this complex metalorganic molecule's efficient enzyme activated catalytic power is still controversial. We have for the first time calculated the electronic structure, Mulliken effective charge and bonding of a whole Vitamin B12 molecule without any structural simplification by first- principles approaches based on density functional theory using structures determined by high resolution X-ray diffraction. A partial density of states analysis shows excellent agreement with X-ray absorption data and has been used successfully to interpret measured optical absorption spectra. Mulliken bonding analysis of B12 and its derivatives reveal noticeable correlations between the two axial ligands which could be exploited by the enzyme to control the catalytic process. Our calculated X-ray near edge structure of B12 and its derivates using Slater's transition state theory are also in good agreement with experiments. The same approach has been applied to other B12 derivatives, ferrocene peptides, and recently DNA molecules.

Experimental and theoretical evaluation on the microenvironmental effect of dimethyl sulfoxide on adrenaline in acid aqueous solution

NASA Astrophysics Data System (ADS)

Yu, Zhang-Yu; Liu, Tao; Guo, Dao-Jun; Liu, Yong-Jun; Liu, Cheng-Bu

2010-12-01

The microenvironmental effect of dimethyl sulfoxide (DMSO) on adrenaline was studied by several approaches including the cyclic voltammetry (CV) of adrenaline at a platinum electrode in acid aqueous solution, the chemical shift of 1H nuclear magnetic resonance ( 1H NMR) of adrenaline, and the change of diffusion coefficient of adrenaline. The experimental results demonstrated that DMSO has significant microenvironmental effect on adrenaline, which was confirmed by the density functional theory (DFT) study on the hydrogen bond (H-bond) complexes of adrenaline with water and DMSO.

Studies of dispersion energy in hydrogen-bonded systems. H2O-HOH, H2O-HF, H3N-HF, HF-HF

NASA Astrophysics Data System (ADS)

Szcześniak, M. M.; Scheiner, Steve

1984-02-01

Dispersion energy is calculated in the systems H2O-HOH, H2O-HF, H3N-HF, and HF-HF as a function of the intermolecular separation using a variety of methods. M≂ller-Plesset perturbation theory to second and third orders is applied in conjunction with polarized basis sets of 6-311G** type and with an extended basis set including a second set of polarization functions (DZ+2P). These results are compared to a multipole expansion of the dispersion energy, based on the Unsöld approximation, carried out to the inverse tenth power of the intermolecular distance. Pairwise evaluation is also carried out using both atom-atom and bond-bond formulations. The MP3/6-311G** results are in generally excellent accord with the leading R-6 term of the multipole expansion. This expansion, if carried out to the R-10 term, reproduces extremely well previously reported dispersion energies calculated via variation-perturbation theory. Little damping of the expansion is required for intermolecular distances equal to or greater than the equilibrium separation. Although the asymptotic behavior of the MP2 dispersion energy is somewhat different than that of the other methods, augmentation of the basis set by a second diffuse set of d functions leads to quite good agreement in the vicinity of the minima. Both the atom-atom and bond-bond parametrization schemes are in good qualitative agreement with the other methods tested. All approaches produce similar dependence of the dispersion energy upon the angular orientation between the two molecules involved in the H bond.

Ferromagnetic bond of Li{sub 10} cluster: An alternative approach in terms of effective ferromagnetic sites

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

Donoso, Roberto; Fuentealba, Patricio, E-mail: pfuentea@hotmail.es, E-mail: cardena@macul.ciencias.uchile.cl; Cárdenas, Carlos, E-mail: pfuentea@hotmail.es, E-mail: cardena@macul.ciencias.uchile.cl

In this work, a model to explain the unusual stability of atomic lithium clusters in their highest spin multiplicity is presented and used to describe the ferromagnetic bonding of high-spin Li{sub 10} and Li{sub 8} clusters. The model associates the (lack of-)fitness of Heisenberg Hamiltonian with the degree of (de-)localization of the valence electrons in the cluster. It is shown that a regular Heisenberg Hamiltonian with four coupling constants cannot fully explain the energy of the different spin states. However, a more simple model in which electrons are located not at the position of the nuclei but at the positionmore » of the attractors of the electron localization function succeeds in explaining the energy spectrum and, at the same time, explains the ferromagnetic bond found by Shaik using arguments of valence bond theory. In this way, two different points of view, one more often used in physics, the Heisenberg model, and the other in chemistry, valence bond, come to the same answer to explain those atypical bonds.« less

Bond Order Conservation Strategies in Catalysis Applied to the NH 3 Decomposition Reaction

DOE PAGES

Yu, Liang; Abild-Pedersen, Frank

2016-12-14

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. Here, we have applied this approach together withmore » linear scaling of adsorption energies to obtain the energetics of the NH 3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. Moreover, this information is used to establish a microkinetic model for the formation of N 2 and H 2, thus providing insight into the components of the reaction that determines the activity.« less

Analysis of the bond-valence method for calculating (29) Si and (31) P magnetic shielding in covalent network solids.

PubMed

Holmes, Sean T; Alkan, Fahri; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2016-07-05

(29) Si and (31) P magnetic-shielding tensors in covalent network solids have been evaluated using periodic and cluster-based calculations. The cluster-based computational methodology employs pseudoatoms to reduce the net charge (resulting from missing co-ordination on the terminal atoms) through valence modification of terminal atoms using bond-valence theory (VMTA/BV). The magnetic-shielding tensors computed with the VMTA/BV method are compared to magnetic-shielding tensors determined with the periodic GIPAW approach. The cluster-based all-electron calculations agree with experiment better than the GIPAW calculations, particularly for predicting absolute magnetic shielding and for predicting chemical shifts. The performance of the DFT functionals CA-PZ, PW91, PBE, rPBE, PBEsol, WC, and PBE0 are assessed for the prediction of (29) Si and (31) P magnetic-shielding constants. Calculations using the hybrid functional PBE0, in combination with the VMTA/BV approach, result in excellent agreement with experiment. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The Halogen Bond in the Design of Functional Supramolecular Materials: Recent Advances

PubMed Central

2013-01-01

Halogen bonding is an emerging noncovalent interaction for constructing supramolecular assemblies. Though similar to the more familiar hydrogen bonding, four primary differences between these two interactions make halogen bonding a unique tool for molecular recognition and the design of functional materials. First, halogen bonds tend to be much more directional than (single) hydrogen bonds. Second, the interaction strength scales with the polarizability of the bond-donor atom, a feature that researchers can tune through single-atom mutation. In addition, halogen bonds are hydrophobic whereas hydrogen bonds are hydrophilic. Lastly, the size of the bond-donor atom (halogen) is significantly larger than hydrogen. As a result, halogen bonding provides supramolecular chemists with design tools that cannot be easily met with other types of noncovalent interactions and opens up unprecedented possibilities in the design of smart functional materials. This Account highlights the recent advances in the design of halogen-bond-based functional materials. Each of the unique features of halogen bonding, directionality, tunable interaction strength, hydrophobicity, and large donor atom size, makes a difference. Taking advantage of the hydrophobicity, researchers have designed small-size ion transporters. The large halogen atom size provided a platform for constructing all-organic light-emitting crystals that efficiently generate triplet electrons and have a high phosphorescence quantum yield. The tunable interaction strengths provide tools for understanding light-induced macroscopic motions in photoresponsive azobenzene-containing polymers, and the directionality renders halogen bonding useful in the design on functional supramolecular liquid crystals and gel-phase materials. Although halogen bond based functional materials design is still in its infancy, we foresee a bright future for this field. We expect that materials designed based on halogen bonding could lead to applications in biomimetics, optics/photonics, functional surfaces, and photoswitchable supramolecules. PMID:23805801

Dual C-H functionalization of N-aryl amines: synthesis of polycyclic amines via an oxidative Povarov approach.

PubMed

Min, Chang; Sanchawala, Abbas; Seidel, Daniel

2014-05-16

Iminium ions generated in situ via copper(I) bromide catalyzed oxidation of N-aryl amines readily undergo [4 + 2] cycloadditions with a range of dienophiles. This method involves the functionalization of both a C(sp(3))-H and a C(sp(2))-H bond and enables the rapid construction of polycyclic amines under relatively mild conditions.

Cobalt catalyzed carbonylation of unactivated C(sp3)–H bonds† †Electronic supplementary information (ESI) available. CCDC 1507203 (2t) & 1507204 (2a). For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc05026c Click here for additional data file. Click here for additional data file.

PubMed Central

Barsu, Nagaraju; Bolli, Shyam Kumar

2017-01-01

A general efficient regioselective cobalt catalyzed carbonylation of unactivated C(sp3)–H bonds of aliphatic amides was demonstrated using atmospheric (1–2 atm) carbon monoxide as a C1 source. This straightforward approach provides access to α-spiral succinimide regioselectively in a good yield. Cobalt catalyzed sp3 C–H bond carbonylation is reported for the first time including the functionalization of (β)-C–H bonds of α-1°, 2°, 3° carbons and even internal (β)-C–H bonds. Our initial mechanistic investigation reveals that the C–H activation step is irreversible and will possibly be the rate determining step. PMID:28451350

Atomic and electronic basis for the serrations of refractory high-entropy alloys

NASA Astrophysics Data System (ADS)

Wang, William Yi; Shang, Shun Li; Wang, Yi; Han, Fengbo; Darling, Kristopher A.; Wu, Yidong; Xie, Xie; Senkov, Oleg N.; Li, Jinshan; Hui, Xi Dong; Dahmen, Karin A.; Liaw, Peter K.; Kecskes, Laszlo J.; Liu, Zi-Kui

2017-06-01

Refractory high-entropy alloys present attractive mechanical properties, i.e., high yield strength and fracture toughness, making them potential candidates for structural applications. Understandings of atomic and electronic interactions are important to reveal the origins for the formation of high-entropy alloys and their structure-dominated mechanical properties, thus enabling the development of a predictive approach for rapidly designing advanced materials. Here, we report the atomic and electronic basis for the valence-electron-concentration-categorized principles and the observed serration behavior in high-entropy alloys and high-entropy metallic glass, including MoNbTaW, MoNbVW, MoTaVW, HfNbTiZr, and Vitreloy-1 MG (Zr41Ti14Cu12.5Ni10Be22.5). We find that the yield strengths of high-entropy alloys and high-entropy metallic glass are a power-law function of the electron-work function, which is dominated by local atomic arrangements. Further, a reliance on the bonding-charge density provides a groundbreaking insight into the nature of loosely bonded spots in materials. The presence of strongly bonded clusters and weakly bonded glue atoms imply a serrated deformation of high-entropy alloys, resulting in intermittent avalanches of defects movement.

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.

Screening based approach and dehydrogenation kinetics for MgH2: Guide to find suitable dopant using first-principles approach.

PubMed

Kumar, E Mathan; Rajkamal, A; Thapa, Ranjit

2017-11-14

First-principles based calculations are performed to investigate the dehydrogenation kinetics considering doping at various layers of MgH 2 (110) surface. Doping at first and second layer of MgH 2 (110) has a significant role in lowering the H 2 desorption (from surface) barrier energy, whereas the doping at third layer has no impact on the barrier energy. Molecular dynamics calculations are also performed to check the bonding strength, clusterization, and system stability. We study in details about the influence of doping on dehydrogenation, considering the screening factors such as formation enthalpy, bulk modulus, and gravimetric density. Screening based approach assist in finding Al and Sc as the best possible dopant in lowering of desorption temperature, while preserving similar gravimetric density and Bulk modulus as of pure MgH 2 system. The electron localization function plot and population analysis illustrate that the bond between Dopant-Hydrogen is mainly covalent, which weaken the Mg-Hydrogen bonds. Overall we observed that Al as dopant is suitable and surface doping can help in lowering the desorption temperature. So layer dependent doping studies can help to find the best possible reversible hydride based hydrogen storage materials.

Silylation of C-H bonds in aromatic heterocycles by an Earth-abundant metal catalyst

NASA Astrophysics Data System (ADS)

Toutov, Anton A.; Liu, Wen-Bo; Betz, Kerry N.; Fedorov, Alexey; Stoltz, Brian M.; Grubbs, Robert H.

2015-02-01

Heteroaromatic compounds containing carbon-silicon (C-Si) bonds are of great interest in the fields of organic electronics and photonics, drug discovery, nuclear medicine and complex molecule synthesis, because these compounds have very useful physicochemical properties. Many of the methods now used to construct heteroaromatic C-Si bonds involve stoichiometric reactions between heteroaryl organometallic species and silicon electrophiles or direct, transition-metal-catalysed intermolecular carbon-hydrogen (C-H) silylation using rhodium or iridium complexes in the presence of excess hydrogen acceptors. Both approaches are useful, but their limitations include functional group incompatibility, narrow scope of application, high cost and low availability of the catalysts, and unproven scalability. For this reason, a new and general catalytic approach to heteroaromatic C-Si bond construction that avoids such limitations is highly desirable. Here we report an example of cross-dehydrogenative heteroaromatic C-H functionalization catalysed by an Earth-abundant alkali metal species. We found that readily available and inexpensive potassium tert-butoxide catalyses the direct silylation of aromatic heterocycles with hydrosilanes, furnishing heteroarylsilanes in a single step. The silylation proceeds under mild conditions, in the absence of hydrogen acceptors, ligands or additives, and is scalable to greater than 100 grams under optionally solvent-free conditions. Substrate classes that are difficult to activate with precious metal catalysts are silylated in good yield and with excellent regioselectivity. The derived heteroarylsilane products readily engage in versatile transformations enabling new synthetic strategies for heteroaromatic elaboration, and are useful in their own right in pharmaceutical and materials science applications.

Assessing the distinguishable cluster approximation based on the triple bond-breaking in the nitrogen molecule

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

Rishi, Varun; Perera, Ajith; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu

2016-03-28

Obtaining the correct potential energy curves for the dissociation of multiple bonds is a challenging problem for ab initio methods which are affected by the choice of a spin-restricted reference function. Coupled cluster (CC) methods such as CCSD (coupled cluster singles and doubles model) and CCSD(T) (CCSD + perturbative triples) correctly predict the geometry and properties at equilibrium but the process of bond dissociation, particularly when more than one bond is simultaneously broken, is much more complicated. New modifications of CC theory suggest that the deleterious role of the reference function can be diminished, provided a particular subset of termsmore » is retained in the CC equations. The Distinguishable Cluster (DC) approach of Kats and Manby [J. Chem. Phys. 139, 021102 (2013)], seemingly overcomes the deficiencies for some bond-dissociation problems and might be of use in quasi-degenerate situations in general. DC along with other approximate coupled cluster methods such as ACCD (approximate coupled cluster doubles), ACP-D45, ACP-D14, 2CC, and pCCSD(α, β) (all defined in text) falls under a category of methods that are basically obtained by the deletion of some quadratic terms in the double excitation amplitude equation for CCD/CCSD (coupled cluster doubles model/coupled cluster singles and doubles model). Here these approximate methods, particularly those based on the DC approach, are studied in detail for the nitrogen molecule bond-breaking. The N{sub 2} problem is further addressed with conventional single reference methods but based on spatial symmetry-broken restricted Hartree–Fock (HF) solutions to assess the use of these references for correlated calculations in the situation where CC methods using fully symmetry adapted SCF solutions fail. The distinguishable cluster method is generalized: 1) to different orbitals for different spins (unrestricted HF based DCD and DCSD), 2) by adding triples correction perturbatively (DCSD(T)) and iteratively (DCSDT-n), and 3) via an excited state approximation through the equation of motion (EOM) approach (EOM-DCD, EOM-DCSD). The EOM-CC method is used to identify lower-energy CC solutions to overcome singularities in the CC potential energy curves. It is also shown that UHF based CC and DC methods behave very similarly in bond-breaking of N{sub 2}, and that using spatially broken but spin preserving SCF references makes the CCSD solutions better than those for DCSD.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

DOE PAGES

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; ...

2016-09-09

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

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

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level.

PubMed

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurélien; Blumberger, Jochen; Elstner, Marcus

2016-10-11

In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated π-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

Construction of a Hierarchical Architecture of Covalent Organic Frameworks via a Postsynthetic Approach.

PubMed

Zhang, Gen; Tsujimoto, Masahiko; Packwood, Daniel; Duong, Nghia Tuan; Nishiyama, Yusuke; Kadota, Kentaro; Kitagawa, Susumu; Horike, Satoshi

2018-02-21

Covalent organic frameworks (COFs) represent an emerging class of crystalline porous materials that are constructed by the assembly of organic building blocks linked via covalent bonds. Several strategies have been developed for the construction of new COF structures; however, a facile approach to fabricate hierarchical COF architectures with controlled domain structures remains a significant challenge, and has not yet been achieved. In this study, a dynamic covalent chemistry (DCC)-based postsynthetic approach was employed at the solid-liquid interface to construct such structures. Two-dimensional imine-bonded COFs having different aromatic groups were prepared, and a homogeneously mixed-linker structure and a heterogeneously core-shell hollow structure were fabricated by controlling the reactivity of the postsynthetic reactions. Solid-state nuclear magnetic resonance (NMR) spectroscopy and transmission electron microscopy (TEM) confirmed the structures. COFs prepared by a postsynthetic approach exhibit several functional advantages compared with their parent phases. Their Brunauer-Emmett-Teller (BET) surface areas are 2-fold greater than those of their parent phases because of the higher crystallinity. In addition, the hydrophilicity of the material and the stepwise adsorption isotherms of H 2 O vapor in the hierarchical frameworks were precisely controlled, which was feasible because of the distribution of various domains of the two COFs by controlling the postsynthetic reaction. The approach opens new routes for constructing COF architectures with functionalities that are not possible in a single phase.

Characterization of Epoxy Functionalized Graphite Nanoparticles and the Physical Properties of Epoxy Matrix Nanocomposites

NASA Technical Reports Server (NTRS)

Miller, Sandi G.; Bauer, Jonathan L.; Maryanski, Michael J.; Heimann, Paula J.; Barlow, Jeremy P.; Gosau, Jan-Michael; Allred, Ronald E.

2010-01-01

This work presents a novel approach to the functionalization of graphite nanoparticles. The technique provides a mechanism for covalent bonding between the filler and matrix, with minimal disruption to the sp2 hybridization of the pristine graphene sheet. Functionalization proceeded by covalently bonding an epoxy monomer to the surface of expanded graphite, via a coupling agent, such that the epoxy concentration was measured as approximately 4 wt.%. The impact of dispersing this material into an epoxy resin was evaluated with respect to the mechanical properties and electrical conductivity of the graphite-epoxy nanocomposite. At a loading as low as 0.5 wt.%, the electrical conductivity was increased by five orders of magnitude relative to the base resin. The material yield strength was increased by 30% and Young s modulus by 50%. These results were realized without compromise to the resin toughness.

Selective oxoanion separation using a tripodal ligand

DOEpatents

Custelcean, Radu; Moyer, Bruce A.; Rajbanshi, Arbin

2016-02-16

The present invention relates to urea-functionalized crystalline capsules self-assembled by sodium or potassium cation coordination and by hydrogen-bonding water bridges to selectively encapsulate tetrahedral divalent oxoanions from highly competitive aqueous alkaline solutions and methods using this system for selective anion separations from industrial solutions. The method involves competitive crystallizations using a tripodal tris(urea) functionalized ligand and, in particular, provides a viable approach to sulfate separation from nuclear wastes.

[Pb(H2O)]2+ and [Pb(OH)]+: four-component density functional theory calculations, correlated scalar relativistic constrained-space orbital variation energy decompositions, and topological analysis.

PubMed

Gourlaouen, Christophe; Piquemal, Jean-Philip; Parisel, Olivier

2006-05-07

Within the scope of studying the molecular implications of the Pb(2+) cation in environmental and polluting processes, this paper reports Hartree-Fock and density functional theory (B3LYP) four-component relativistic calculations using an all-electron basis set applied to [Pb(H(2)O)](2+) and [Pb(OH)](+), two complexes expected to be found in the terrestrial atmosphere. It is shown that full-relativistic calculations validate the use of scalar relativistic approaches within the framework of density functional theory. [Pb(H(2)O)](2+) is found C(2v) at any level of calculations whereas [Pb(OH)](+) can be found bent or linear depending of the computational methodology used. When C(s) is found the barrier to inversion through the C(infinityv) structure is very low, and can be overcome at high enough temperature, making the molecule floppy. In order to get a better understanding of the bonding occurring between the Pb(2+) cation and the H(2)O and OH(-) ligands, natural bond orbital and atoms-in-molecule calculations have been performed. These approaches are supplemented by a topological analysis of the electron localization function. Finally, the description of these complexes is refined using constrained-space orbital variation complexation energy decompositions.

Block correlated second order perturbation theory with a generalized valence bond reference function.

PubMed

Xu, Enhua; Li, Shuhua

2013-11-07

The block correlated second-order perturbation theory with a generalized valence bond (GVB) reference (GVB-BCPT2) is proposed. In this approach, each geminal in the GVB reference is considered as a "multi-orbital" block (a subset of spin orbitals), and each occupied or virtual spin orbital is also taken as a single block. The zeroth-order Hamiltonian is set to be the summation of the individual Hamiltonians of all blocks (with explicit two-electron operators within each geminal) so that the GVB reference function and all excited configuration functions are its eigenfunctions. The GVB-BCPT2 energy can be directly obtained without iteration, just like the second order Mo̸ller-Plesset perturbation method (MP2), both of which are size consistent. We have applied this GVB-BCPT2 method to investigate the equilibrium distances and spectroscopic constants of 7 diatomic molecules, conformational energy differences of 8 small molecules, and bond-breaking potential energy profiles in 3 systems. GVB-BCPT2 is demonstrated to have noticeably better performance than MP2 for systems with significant multi-reference character, and provide reasonably accurate results for some systems with large active spaces, which are beyond the capability of all CASSCF-based methods.

Emphasizing the Significance of Electrostatic Interactions in Chemical Bonding

ERIC Educational Resources Information Center

Venkataraman, Bhawani

2017-01-01

This paper describes a pedagogical approach to help students understand chemical bonding by emphasizing the importance of electrostatic interactions between atoms. The approach draws on prior studies that have indicated many misconceptions among students in understanding the nature of the chemical bond and energetics associated with bond formation…

Effect of dispersion correction on the Au(1 1 1)-H2O interface: A first-principles study

NASA Astrophysics Data System (ADS)

Nadler, Roger; Sanz, Javier Fdez.

2012-09-01

A theoretical study of the H2O-Au(1 1 1) interface based on first principles density functional theory (DFT) calculations with and without inclusion of dispersion correction is reported. Three different computational approaches are considered. First, the standard generalized gradient approximation (GGA) functional PBE is employed. Second, an additional energy term is further included that adds a semi-empirically derived dispersion correction (PBE-D2), and, finally, a recently proposed functional that includes van der Waals (vdW) interactions directly in its functional form (optB86b-vdW) was used to represent the state-of-the art of DFT functionals. The monomeric water adsorption was first considered in order to explore the dependency of geometry on the details of the model slab used to represent it (size, thickness, coverage). When the dispersion corrections are included the Au-H2O interaction is stronger, as manifested by the smaller dAu-O and stronger adsorption energies. Additionally, the interfacial region between Au(1 1 1) slab surfaces and a liquid water layer was investigated with Born-Oppenheimer molecular dynamics (BOMD) using the same functionals. Two or three interfacial orientations can be determined, depending on the theoretical methodology applied. Closest to the surface, H2O is adsorbed O-down, whereas further away it is oriented with one OH bond pointing to the surface and the molecular plane parallel to the normal direction. For the optB86b-vdW functional a third orientation is found where one H atom points into the bulk water layer and the second OH bond is oriented parallel to the metal surface. As for the water density in the first adsorption layer we find a very small increase of roughly 8%. From the analysis of vibrational spectra a weakening of the H-bond network is observed upon the inclusion of the Au(1 1 1) slab, however, no disruption of H-bonds is observed. While the PBE and PBE-D2 spectra are very similar, the optB86b-vdW spectrum shows that the H-bonds are even more weakened.

Functionalization of P4 through Direct P-C Bond Formation.

PubMed

Borger, Jaap E; Ehlers, Andreas W; Slootweg, J Chris; Lammertsma, Koop

2017-09-04

Research on chlorine-free conversions of P 4 into organophosphorus compounds (OPCs) has a long track record, but methods that allow desirable, direct P-C bond formations have only recently emerged. These include the use of metal organyls, carbenes, carboradicals, and photochemical approaches. The versatile product scope enables the preparation of both industrially relevant organophosphorus compounds, as well as a broad range of intriguing new compound classes. Herein we provide a concise overview of recent breakthroughs and outline the acquired fundamental insights to aid future developments. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio theory and modeling of water.

PubMed

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C; Calegari Andrade, Marcos F; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L; Perdew, John P; Wu, Xifan

2017-10-10

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I h at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

Ab initio theory and modeling of water

PubMed Central

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C.; Calegari Andrade, Marcos F.; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L.; Perdew, John P.; Wu, Xifan

2017-01-01

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner. PMID:28973868

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

On the nature of interactions in the F2 OXe(…) NCCH3 complex: Is there the Xe(IV)N bond?

PubMed

Makarewicz, Emilia; Lundell, Jan; Gordon, Agnieszka J; Berski, Slawomir

2016-07-01

Nature of the bonding in isolated XeOF2 molecule and F2 OXe(…) NCCH3 complexes have been studied in the gas phase (0 K) using Quantum Chemical Topology methods. The wave functions have been approximated at the MP2 and DFT levels of calculations, using the APFD, B3LYP, M062X, and B2PLYP functionals with the GD3 dispersion correction. The nature of the formal XeO bond in the XeOF2 monomer depends on the basis set used (all-electron vs. the ecp-28 approximation for Xe). Within the all-electron basis set approach the bond is represented by two bonding attractors, Vi = 1,2 (Xe,O), with total population of about 1.06e and highly delocalized electron density in both bonding basins. No bonding basins are observed using the ecp-28 approximation. These results shows that the nature of xenon-oxygen is complicated and may be described with mesomeric equilibrium of the Lewis representations: Xe((+)) O((-)) and Xe((-)) O((+)) . For both the xenon-oxygen and xenon-fluorine interactions the charge-shift model can be applied. The F2 OXe(…) NCCH3 complex exists in two structures: "parallel," stabilized by non-covalent C(…) O and Xe(…) N interactions and "linear" stabilized by the Xe(…) N interaction. Topological analysis of ELF shows that the F2 OXe(…) NCCH3 molecule appears as a weakly bound intermolecular complex. Intermolecular interaction energy components have also been studied using Symmetry Adapted Perturbation Theory. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Modeling single molecule junction mechanics as a probe of interface bonding

NASA Astrophysics Data System (ADS)

Hybertsen, Mark S.

2017-03-01

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. A set of exemplary model junction structures has been analyzed using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond to the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N-Au and S-Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. The results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.

Modeling single molecule junction mechanics as a probe of interface bonding

DOE PAGES

Hybertsen, Mark S.

2017-03-07

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Modeling single molecule junction mechanics as a probe of interface bonding

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

Hybertsen, Mark S.

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

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.

Evolution of C−H Bond Functionalization from Methane to Methodology

PubMed Central

2016-01-01

This Perspective presents the fundamental principles, the elementary reactions, the initial catalytic systems, and the contemporary catalysts that have converted C−H bond functionalization from a curiosity to a reality for synthetic chemists. Many classes of elementary reactions involving transition-metal complexes cleave C−H bonds at typically unreactive positions. These reactions, coupled with a separate or simultaneous functionalization process lead to products containing new C−C, C−N, and C−O bonds. Such reactions were initially studied for the conversion of light alkanes to liquid products, but they have been used (and commercialized in some cases) most often for the synthesis of the more complex structures of natural products, medicinally active compounds, and aromatic materials. Such a change in direction of research in C−H bond functionalization is remarkable because the reactions must occur at an unactivated C−H bond over functional groups that are more reactive than the C−H bond toward classical reagents. The scope of reactions that form C−C bonds or install functionality at an unactivated C−H bond will be presented, and the potential future utility of these reactions will be discussed. PMID:26566092

Of cuts and cracks: data analytics on constrained graphs for early prediction of failure in cementitious materials

NASA Astrophysics Data System (ADS)

Kahagalage, Sanath; Tordesillas, Antoinette; Nitka, Michał; Tejchman, Jacek

2017-06-01

Using data from discrete element simulations, we develop a data analytics approach using network flow theory to study force transmission and failure in a `dog-bone' concrete specimen submitted to uniaxial tension. With this approach, we establish the extent to which the bottlenecks, i.e., a subset of contacts that impedes flow and are prone to becoming overloaded, can predict the location of the ultimate macro-crack. At the heart of this analysis is a capacity function that quantifies, in relative terms, the maximum force that can be transmitted through the different contacts or edges in the network. Here we set this function to be solely governed by the size of the contact area between the deformable spherical grains. During all the initial stages of the loading history, when no bonds are broken, we find the bottlenecks coincide consistently with, and therefore predict, the location of the crack that later forms in the failure regime after peak force. When bonds do start to break, they are spread throughout the specimen: in, near, and far from, the bottlenecks. In one stage leading up to peak force, bonds collectively break in the lower portion of the specimen, momentarily shifting the bottlenecks to this location. Just before and around peak force, however, the bottlenecks return to their original location and remain there until the macro-crack emerges right along the bottlenecks.

Microsolvation effect and hydrogen-bonding pattern of taurine-water TA-(H2O)n (n = 1-3) complexes.

PubMed

Dai, Yumei; Wang, Yuhua; Huang, Zhengguo; Wang, Hongke; Yu, Lei

2012-01-01

The microsolvation of taurine (TA) with one, two or three water molecules was investigated by a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen bond (H-bond) interaction characteristics in TA-(H(2)O)(n) (n = 1-3) complexes. The results showed that the intramolecular H-bond formed between the hydroxyl and the N atom of TA are retained in most TA-(H(2)O)(n) (n = 1-3) complexes, and are strengthened via cooperative effects among multiple H-bonds from n = 1-3. A trend of proton transformation exists from the hydroxyl to the N atom, which finally results in the cleavage of the origin intramolecular H-bond and the formation of a new intramolecular H-bond between the amino and the O atom of TA. Therefore, the most stable TA-(H(2)O)(3) complex becomes a zwitterionic complex rather than a neutral type. A many-body interaction analysis showed that the major contributors to the binding energies for complexes are the two-body energies, while three-body energies and relaxation energies make significant contributions to the binding energies for some complexes, whereas the four-body energies are too small to be significant.

From a remarkable manifestation of polar effects in a radical fragmentation to the convergent synthesis of highly functionalized ketones.

PubMed

Debien, Laurent; Zard, Samir Z

2013-03-13

A new radical addition/C-C bond fragmentation process is reported. Vinyl carbinols derived from 2-methyl-2-phenylpropanal react with radicals generated from xanthates to give the corresponding ketones. The radical cleavage reaction proceeds under mild conditions, in good to high yield, and in the presence of the unprotected carbinol. Highly functionalized 1,5-diketones and pyridines are readily available using this approach.

Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins.

PubMed

Das, Sreetama; Bhadra, Pratiti; Ramakumar, Suryanarayanarao; Pal, Debnath

2017-08-04

cis-Peptide bonds, whose occurrence in proteins is rare but evolutionarily conserved, are implicated to play an important role in protein function. This has led to their previous use in a homology-independent, fragment-match-based protein function annotation method. However, proteins are not static molecules; dynamics is integral to their activity. This is nicely epitomized by the geometric isomerization of cis-peptide to trans form for molecular activity. Hence we have incorporated both static (cis-peptide) and dynamics information to improve the prediction of protein molecular function. Our results show that cis-peptide information alone cannot detect functional matches in cases where cis-trans isomerization exists but 3D coordinates have been obtained for only the trans isomer or when the cis-peptide bond is incorrectly assigned as trans. On the contrary, use of dynamics information alone includes false-positive matches for cases where fragments with similar secondary structure show similar dynamics, but the proteins do not share a common function. Combining the two methods reduces errors while detecting the true matches, thereby enhancing the utility of our method in function annotation. A combined approach, therefore, opens up new avenues of improving existing automated function annotation methodologies.

Autobiographical memory functions in young Japanese men and women.

PubMed

Maki, Yoichi; Kawasaki, Yayoi; Demiray, Burcu; Janssen, Steve M J

2015-01-01

The present study examined whether the three major functions of autobiographical memory observed in Western societies (i.e., directing-behaviour, social-bonding and self-continuity) also exist in an East Asian society. Two self-report measures were used to assess the autobiographical memory functions of Japanese men and women. Japanese young adults (N = 451, ages 17-28 years) first completed the original Thinking About Life Experiences (TALE) Questionnaire. They subsequently received three TALE items that represented memory functions and attempted to recall a specific instance of memory recall for each item. Confirmatory factor analyses on the TALE showed that the three functions were replicated in the current sample. However, Japanese participants reported lower levels of all three functions than American participants in a previous study. We also explored whether there was an effect of gender in this Japanese sample. Women reported higher levels of the self-continuity and social-bonding functions than men. Finally, participants recalled more specific instances of memory recall for the TALE items that had received higher ratings on the TALE, suggesting that the findings on the first measure were supported by the second measure. Results are discussed in relation to the functional approach to autobiographical memory in a cross-cultural context.

In search of efficient 5-endo-dig cyclization of a carbon-centered radical: 40 years from a prediction to another success for the Baldwin rules.

PubMed

Alabugin, Igor V; Timokhin, Vitaliy I; Abrams, Jason N; Manoharan, Mariappan; Abrams, Rachel; Ghiviriga, Ion

2008-08-20

Despite being predicted to be stereoelectronically favorable by the Baldwin rules, efficient formation of a C-C bond through a 5-endo-dig radical cyclization remained unknown for more than 40 years. This work reports a remarkable increase in the efficiency of this process upon beta-Ts substitution, which led to the development of an expedient approach to densely functionalized cyclic 1,3-dienes. Good qualitative agreement between the increased efficiency and stereoselectivity for the 5-endo-dig cyclization of Ts-substituted vinyl radicals and the results of density functional theory analysis further confirms the utility of computational methods in the design of new radical processes. Although reactions of Br atoms generated through photochemical Ts-Br bond homolysis lead to the formation of cyclic dibromide side products, the yields of target bromosulfones in the photochemically induced reactions can be increased by recycling the dibromide byproduct into the target bromosulfones through a sequence of addition/elimination reactions at the exocyclic double bond. Discovery of a relatively efficient radical 5-endo-dig closure, accompanied by a C-C bond formation, provides further support to stereoelectronic considerations at the heart of the Baldwin rules and fills one of the last remaining gaps in the arsenal of radical cyclizations.

Diazonium functionalized graphene: microstructure, electric, and magnetic properties.

PubMed

Huang, Ping; Jing, Long; Zhu, Huarui; Gao, Xueyun

2013-01-15

The unique honeycomb lattice structure of graphene gives rise to its outstanding electronic properties such as ultrahigh carrier mobility, ballistic transport, and more. However, a crucial obstacle to its use in the electronics industry is its lack of an energy bandgap. A covalent chemistry strategy could overcome this problem, and would have the benefits of being highly controllable and stable in the ambient environment. One possible approach is aryl diazonium functionalization. In this Account, we investigate the micromolecular/lattice structure, electronic structure, and electron-transport properties of nitrophenyl-diazonium-functionalized graphene. We find that nitrophenyl groups mainly adopt random and inhomogeneous configurations on the graphene basal plane, and that their bonding with graphene carbon atoms leads to slight elongation of the graphene lattice spacing. By contrast, hydrogenated graphene has a compressed lattice. Low levels of functionalization suppressed the electric conductivity of the resulting functionalized graphene, while highly functionalized graphene showed the opposite effect. This difference arises from the competition between the charge transfer effect and the scattering enhancement effect introduced by nitrophenyl groups bonding with graphene carbon atoms. Detailed electron transport measurements revealed that the nitrophenyl diazonium functionalization locally breaks the symmetry of graphene lattice, which leads to an increase in the density of state near the Fermi level, thus increasing the carrier density. On the other hand, the bonded nitrophenyl groups act as scattering centers, lowering the mean free path of the charge carriers and suppressing the carrier mobility. In rare cases, we observed ordered configurations of nitrophenyl groups in local domains on graphene flakes due to fluctuations in the reaction processes. We describe one example of such a superlattice, with a lattice constant nearly twice of that of pristine graphene. We performed comprehensive theoretical calculations to investigate the lattice and the electronic structure of the superlattice structure. Our results reveal that it is a thermodynamically stable, spin-polarized semiconductor with a bandgap of ∼0.5 eV. Our results demonstrate the possibility of controlling graphene's electronic properties using aryl diazonium functionalization. Asymmetric addition of aryl groups to different sublattices of graphene is a promising approach for producing ferromagnetic, semiconductive graphene, which will have broad applications in the electronic industry.

A new face of phenalenyl-based radicals in the transition metal-free C-H arylation of heteroarenes at room temperature: trapping the radical initiator via C-C σ-bond formation.

PubMed

Ahmed, Jasimuddin; P, Sreejyothi; Vijaykumar, Gonela; Jose, Anex; Raj, Manthan; Mandal, Swadhin K

2017-11-01

The radical-mediated transition metal-free approach for the direct C-H bond functionalization of arenes is considered as a cost effective alternative to transition metal-based catalysis. An organic ligand-based radical plays a key role by generating an aryl radical which undergoes a subsequent functionalization process. The design principle of the present study takes advantage of a relatively stable odd alternant hydrocarbon-based phenalenyl (PLY) radical. In this study, the first transition metal-free catalyzed direct C-H arylation of a variety of heteroarenes such as azoles, furan, thiophene and pyridine at room temperature has been reported using a phenalenyl-based radical without employing any photoactivation step. This protocol has been successfully applied to the gram scale synthesis of core moieties of bioactive molecules. The phenalenyl-based radical initiator has been characterized crystallographically by trapping it via the formation of a C-C σ-bond between the phenalenyl radical and solvent-based radical species.

Bio-inspired Self-healing Composite Hydrogel with Iron Oxide Nanoparticle as Coordination Crosslinker

NASA Astrophysics Data System (ADS)

Li, Qiaochu; Barret, Devin G.; Messersmith, Phillip B.; Holten-Andersen, Niels

2014-03-01

Polymer-nanoparticle (NP) composites have attracted renewed attention due to enhanced mechanical strength combined with various functionalities, but controlling the interfacial chemistry between NPs and polymer matrix, which is crucial for the composite's mechanical behavior, remains a major challenge. Inspired by the adhesion chemistry of mussel fibers, we investigated a novel approach to incorporate Fe3O4 NPs into hydrogel matrix. A polyethylene glycol polymer is designed with both ends conjugated by catechol groups, which have strong coordination affinity to Fe. The polymer network is crosslinked via coordination bonding at the surface of Fe3O4 NPs, yielding a stiff nanocomposite hydrogel. Due to the reversible nature of coordination bonding, the hydrogel presents self-healing behavior. Oscillatory rheology allows comparative kinetic studies of self-healing driven by catechol bonding at Fe3O4 NP interfaces and by catechol-Fe3+ coordination complexes. Furthermore, the superparamagnetic property of Fe3O4 NP is preserved after gelation, allowing for response to external stimuli. This gelation motif can serve as a versatile platform for tuning functional and mechanical properties for future polymer nanocomposite materials.

Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

PubMed

Moon, Jiwon; Kim, Joonghan

2016-09-29

Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana.

PubMed

Navarro-Retamal, Carlos; Bremer, Anne; Alzate-Morales, Jans; Caballero, Julio; Hincha, Dirk K; González, Wendy; Thalhammer, Anja

2016-10-07

The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain α-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40%) or prevented (100%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state.

Iodine versus Bromine Functionalization for Bottom-Up Graphene Nanoribbon Growth: Role of Diffusion

DOE PAGES

Bronner, Christopher; Marangoni, Tomas; Rizzo, Daniel J.; ...

2017-08-08

Deterministic bottom-up approaches for synthesizing atomically well-defined graphene nanoribbons (GNRs) largely rely on the surface-catalyzed activation of selected labile bonds in a molecular precursor followed by step-growth polymerization and cyclodehydrogenation. While the majority of successful GNR precursors rely on the homolytic cleavage of thermally labile C–Br bonds, the introduction of weaker C–I bonds provides access to monomers that can be polymerized at significantly lower temperatures, thus helping to increase the flexibility of the GNR synthesis process. Scanning tunneling microscopy imaging of molecular precursors, activated intermediates, and polymers resulting from stepwise thermal annealing of both Br and I substituted precursors formore » chevron GNRs reveals that the polymerization of both precursors proceeds at similar temperatures on Au(111). Finally, this surprising observation is consistent with diffusion-controlled polymerization of the surface-stabilized radical intermediates that emerge from homolytic cleavage of either the C–Br or the C–I bonds.« less

Some aspects of radical cascade and relay reactions

PubMed Central

Quiclet-Sire, Béatrice; Zard, Samir Z.

2017-01-01

The ability to create carbon–carbon bonds is at the heart of organic synthesis. Radical processes are particularly apt at creating such bonds, especially in cascade or relay sequences where more than one bond is formed, allowing for a rapid assembly of complex structures. In the present brief overview, examples taken from the authors' laboratory will serve to illustrate the strategic impact of radical-based approaches on synthetic planning. Transformations involving nitrogen-centred radicals, electron transfer from metallic nickel and the reversible degenerative exchange of xanthates will be presented and discussed. The last method has proved to be a particularly powerful tool for the intermolecular creation of carbon–carbon bonds by radical additions even to unactivated alkenes. Various functional groups can be brought into the same molecule in a convergent manner and made to react together in order to further increase the structural complexity. One important benefit of this chemistry is the so-called RAFT/MADIX technology for the manufacture of block copolymers of almost any desired architecture. PMID:28484329

Chapter 5 Multiple, Localized, and Delocalized/Conjugated Bonds in the Orbital Communication Theory of Molecular Systems

NASA Astrophysics Data System (ADS)

Nalewajski, Roman F.

Information theory (IT) probe of the molecular electronic structure, within the communication theory of chemical bonds (CTCB), uses the standard entropy/information descriptors of the Shannon theory of communication to characterize a scattering of the electronic probabilities and their information content throughout the system chemical bonds generated by the occupied molecular orbitals (MO). These "communications" between the basis-set orbitals are determined by the two-orbital conditional probabilities: one- and two-electron in character. They define the molecular information system, in which the electron-allocation "signals" are transmitted between various orbital "inputs" and "outputs". It is argued, using the quantum mechanical superposition principle, that the one-electron conditional probabilities are proportional to the squares of corresponding elements of the charge and bond-order (CBO) matrix of the standard LCAO MO theory. Therefore, the probability of the interorbital connections in the molecular communication system is directly related to Wiberg's quadratic covalency indices of chemical bonds. The conditional-entropy (communication "noise") and mutual-information (information capacity) descriptors of these molecular channels generate the IT-covalent and IT-ionic bond components, respectively. The former reflects the electron delocalization (indeterminacy) due to the orbital mixing, throughout all chemical bonds in the system under consideration. The latter characterizes the localization (determinacy) in the probability scattering in the molecule. These two IT indices, respectively, indicate a fraction of the input information lost in the channel output, due to the communication noise, and its surviving part, due to deterministic elements in probability scattering in the molecular network. Together, these two components generate the system overall bond index. By a straightforward output reduction (condensation) of the molecular channel, the IT indices of molecular fragments, for example, localized bonds, functional groups, and forward and back donations accompanying the bond formation, and so on, can be extracted. The flow of information in such molecular communication networks is investigated in several prototype molecules. These illustrative (model) applications of the orbital communication theory of chemical bonds (CTCB) deal with several classical issues in the electronic structure theory: atom hybridization/promotion, single and multiple chemical bonds, bond conjugation, and so on. The localized bonds in hydrides and delocalized [pi]-bonds in simple hydrocarbons, as well as the multiple bonds in CO and CO2, are diagnosed using the entropy/information descriptors of CTCB. The atom promotion in hydrides and bond conjugation in [pi]-electron systems are investigated in more detail. A major drawback of the previous two-electron approach to molecular channels, namely, two weak bond differentiation in aromatic systems, has been shown to be remedied in the one-electron approach.

Adsorption and dissociation of molecular oxygen on α-Pu (0 2 0) surface: A density functional study

NASA Astrophysics Data System (ADS)

Wang, Jianguang; Ray, Asok K.

2011-09-01

Molecular and dissociative oxygen adsorptions on the α-Pu (0 2 0) surface have been systematically studied using the full-potential linearized augmented-plane-wave plus local orbitals (FP-LAPW+lo) basis method and the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional. Chemisorption energies have been optimized for the distance of the admolecule from the Pu surface and the bond length of O-O atoms for four adsorption sites and three approaches of O 2 admolecule to the (0 2 0) surface. Chemisorption energies have been calculated at the scalar relativistic level with no spin-orbit coupling (NSOC) and at the fully relativistic level with spin-orbit coupling (SOC). Dissociative adsorptions are found at the two horizontal approaches (O 2 is parallel to the surface and perpendicular/parallel to a lattice vector). Hor2 (O 2 is parallel to the surface and perpendicular to a lattice vector) approach at the one-fold top site is the most stable adsorption site, with chemisorption energies of 8.048 and 8.415 eV for the NSOC and SOC cases, respectively, and an OO separation of 3.70 Å. Molecular adsorption occurs at the Vert (O 2 is vertical to the surface) approach of each adsorption site. The calculated work functions and net spin magnetic moments, respectively, increase and decrease in all cases upon chemisorption compared to the clean surface. The partial charges inside the muffin-tins, the difference charge density distributions, and the local density of states have been used to investigate the Pu-admolecule electronic structures and bonding mechanisms.

Direct reconstruction of the two-dimensional pair distribution function in partially ordered systems with angular correlations.

PubMed

Zaluzhnyy, I A; Kurta, R P; Menushenkov, A P; Ostrovskii, B I; Vartanyants, I A

2016-09-01

An x-ray scattering approach to determine the two-dimensional (2D) pair distribution function (PDF) in partially ordered 2D systems is proposed. We derive relations between the structure factor and PDF that enable quantitative studies of positional and bond-orientational (BO) order in real space. We apply this approach in the x-ray study of a liquid crystal (LC) film undergoing the smectic-A-hexatic-B phase transition, to analyze the interplay between the positional and BO order during the temperature evolution of the LC film. We analyze the positional correlation length in different directions in real space.

Metal-Free Oxidative C-C Bond Formation through C-H Bond Functionalization.

PubMed

Narayan, Rishikesh; Matcha, Kiran; Antonchick, Andrey P

2015-10-12

The formation of C-C bonds embodies the core of organic chemistry because of its fundamental application in generation of molecular diversity and complexity. C-C bond-forming reactions are well-known challenges. To achieve this goal through direct functionalization of C-H bonds in both of the coupling partners represents the state-of-the-art in organic synthesis. Oxidative C-C bond formation obviates the need for prefunctionalization of both substrates. This Minireview is dedicated to the field of C-C bond-forming reactions through direct C-H bond functionalization under completely metal-free oxidative conditions. Selected important developments in this area have been summarized with representative examples and discussions on their reaction mechanisms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional group placement in protein binding sites: a comparison of GRID and MCSS

NASA Astrophysics Data System (ADS)

Bitetti-Putzer, Ryan; Joseph-McCarthy, Diane; Hogle, James M.; Karplus, Martin

2001-10-01

One approach to combinatorial ligand design begins by determining optimal locations (i.e., local potential energy minima) for functional groups in the binding site of a target macromolecule. MCSS and GRID are two methods, based on significantly different algorithms, which are used for this purpose. A comparison of the two methods for the same functional groups is reported. Calculations were performed for nonpolar and polar functional groups in the internal hydrophobic pocket of the poliovirus capsid protein, and on the binding surface of the src SH3 domain. The two approaches are shown to agree qualitatively; i.e., the global characteristics of the functional group maps generated by MCSS and GRID are similar. However, there are significant differences in the relative interaction energies of the two sets of minima, a consequence of the different functional form used to evaluate polar interactions (electrostatics and hydrogen bonding) in the two methods. The single sphere representation used by GRID affords only positional information, supplemented by the identification of hydrogen bonding interactions. By contrast, the multi-atom representation of most MCSS groups yields in both positional and orientational information. The two methods are most similar for small functional groups, while for larger functional groups MCSS yields results consistent with GRID but superior in detail. These results are in accord with the somewhat different purposes for which the two methods were developed. GRID has been used mainly to introduce functionalities at specific positions in lead compounds, in which case the orientation is predetermined by the structure of the latter. The orientational information provided by MCSS is important for its use in the de novo design of large, multi-functional ligands, as well as for improving lead compounds.

Modeling the self-assembly of functionalized fullerenes on solid surfaces using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Bubnis, Gregory J.

Since their discovery 25 years ago, carbon fullerenes have been widely studied for their unique physicochemical properties and for applications including organic electronics and photovoltaics. For these applications it is highly desirable for crystalline fullerene thin films to spontaneously self-assemble on surfaces. Accordingly, many studies have functionalized fullerenes with the aim of tailoring their intermolecular interactions and controlling interactions with the solid substrate. The success of these rational design approaches hinges on the subtle interplay of intermolecular forces and molecule-substrate interactions. Molecular modeling is well-suited to studying these interactions by directly simulating self-assembly. In this work, we consider three different fullerene functionalization approaches and for each approach we carry out Monte Carlo simulations of the self-assembly process. In all cases, we use a "coarse-grained" molecular representation that preserves the dominant physical interactions between molecules and maximizes computational efficiency. The first approach we consider is the traditional gold-thiolate SAM (self-assembled monolayer) strategy which tethers molecules to a gold substrate via covalent sulfur-gold bonds. For this we study an asymmetric fullerene thiolate bridged by a phenyl group. Clusters of 40 molecules are simulated on the Au(111) substrate at different temperatures and surface coverage densities. Fullerenes and S atoms are found to compete for Au(111) surface sites, and this competition prevents self-assembly of highly ordered monolayers. Next, we investigate self-assembled monolayers formed by fullerenes with hydrogen-bonding carboxylic acid substituents. We consider five molecules with different dimensions and symmetries. Monte Carlo cooling simulations are used to find the most stable solid structures of clusters adsorbed to Au(111). The results show cases where fullerene-Au(111) attraction, fullerene close-packing, and hydrogen-bonding interactions can cooperate to guide self-assembly or compete to hinder it. Finally, we consider three bis-fullerene molecules, each with a different "bridging group" covalently joining two fullerenes. To effectively study the competing "standing-up" and "lying-down" morphologies, we use Monte Carlo simulations in conjunction with replica exchange and force field biasing methods. For clusters adsorbed to smooth model surfaces, we determine free energy landscapes and demonstrate their utility for rationalizing and predicting self-assembly.

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.

Energy decomposition analysis of single bonds within Kohn-Sham density functional theory.

PubMed

Levine, Daniel S; Head-Gordon, Martin

2017-11-28

An energy decomposition analysis (EDA) for single chemical bonds is presented within the framework of Kohn-Sham density functional theory based on spin projection equations that are exact within wave function theory. Chemical bond energies can then be understood in terms of stabilization caused by spin-coupling augmented by dispersion, polarization, and charge transfer in competition with destabilizing Pauli repulsions. The EDA reveals distinguishing features of chemical bonds ranging across nonpolar, polar, ionic, and charge-shift bonds. The effect of electron correlation is assessed by comparison with Hartree-Fock results. Substituent effects are illustrated by comparing the C-C bond in ethane against that in bis(diamantane), and dispersion stabilization in the latter is quantified. Finally, three metal-metal bonds in experimentally characterized compounds are examined: a [Formula: see text]-[Formula: see text] dimer, the [Formula: see text]-[Formula: see text] bond in dizincocene, and the Mn-Mn bond in dimanganese decacarbonyl.

The role of functional monomers in bonding to enamel: acid-base resistant zone and bonding performance.

PubMed

Li, Na; Nikaido, Toru; Takagaki, Tomohiro; Sadr, Alireza; Makishi, Patricia; Chen, Jihua; Tagami, Junji

2010-09-01

To investigate the effects of two functional monomers on caries-inhibition potential and bond strength of two-step self-etching adhesive systems to enamel. Clearfil SE Bond and similar experimental formulations different in the functional monomer were used. Four combinations of primer and bonding agents were evaluated: (1) Clearfil SE Bond which contains MDP in both primer and bonding (M-M); (2) Clearfil SE Bond primer and Phenyl-P in bonding (M-P); (3) Phenyl-P in primer and Clearfil SE Bond bonding (P-M); (4) Phenyl-P in primer and bonding (P-P). Ground buccal enamel surfaces of human sound premolars were treated with one of the systems and the bonded interface was exposed to an artificial demineralising solution (pH 4.5) for 4.5 h, and then 5% NaOCl with ultrasonication for 30 min. After argon-ion etching, the interfacial ultrastructure was observed using SEM. Micro-shear bond strength to enamel was measured for all groups and results were analysed using one-way ANOVA and Turkey's HSD, while failure modes were analysed by chi-square test. An acid-base resistant zone (ABRZ) was found with all adhesive systems containing MDP either in primer or bond; however, ultramorphology and crystallite arrangement in the ABRZ were different among groups. P-P was the only group devoid of this protective zone. Micro-shear bond strength in M-M was significantly higher than those in M-P, P-M and P-P, while the latter three were not different from each other. Failure modes were significantly different (p<0.05). Functional monomers in two-step self-etching systems influence both the bonding performance and the formation of ABRZ on enamel. Copyright 2010 Elsevier Ltd. All rights reserved.

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.

Cyclization Reactions through DDQ-Mediated Vinyl Oxazolidinone Oxidation

PubMed Central

Liu, Lei; Floreancig, Paul E.

2009-01-01

Vinyl oxazolidinones react with DDQ to form α,β-unsaturated acyliminium ions in a new method for forming electrophiles under oxidative conditions. Appended nucleophiles undergo 1,4-addition reactions with these intermediates to form cyclic vinyl oxazolidinones with good levels of diastereocontrol, highlighting a new approach to utilizing oxidative carbon–hydrogen bond functionalization to increase molecular complexity. PMID:19552390

Theoretical Studies of Chemical Reactions following Electronic Excitation

NASA Technical Reports Server (NTRS)

Chaban, Galina M.

2003-01-01

The use of multi-configurational wave functions is demonstrated for several processes: tautomerization reactions in the ground and excited states of the DNA base adenine, dissociation of glycine molecule after electronic excitation, and decomposition/deformation of novel rare gas molecules HRgF. These processes involve bond brealung/formation and require multi-configurational approaches that include dynamic correlation.

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.

Anatase-rutile phase transformation of titanium dioxide bulk material: a DFT + U approach

NASA Astrophysics Data System (ADS)

Vu, Nam H.; Le, Hieu V.; Cao, Thi M.; Pham, Viet V.; Le, Hung M.; Nguyen-Manh, Duc

2012-10-01

The anatase-rutile phase transformation of TiO2 bulk material is investigated using a density functional theory (DFT) approach in this study. According to the calculations employing the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional with the Vanderbilt ultrasoft pseudopotential, it is suggested that the anatase phase is more energetically stable than rutile, which is in variance with the experimental observations. Consequently, the DFT + U method is employed in order to predict the correct structural stability in titania from electronic-structure-based total energy calculations. The Hubbard U term is determined by examining the band structure of rutile with various values of U from 3 to 10 eV. At U = 5 eV, a theoretical bandgap for rutile is obtained as 3.12 eV, which is in very good agreement with the reported experimental bandgap. Hence, we choose the DFT + U method (with U = 5 eV) to investigate the transformation pathway using the newly-developed solid-state nudged elastic band (ss-NEB) method, and consequently obtain an intermediate transition structure that is 9.794 eV per four-TiO2 above the anatase phase. When the Ti-O bonds in the transition state are examined using charge density analysis, seven Ti-O bonds (out of 24 bonds in the anatase unit cell) are broken, and this result is in excellent agreement with a previous experimental study (Penn and Banfield 1999 Am. Miner. 84 871-6).

Communication: xDH double hybrid functionals can be qualitatively incorrect for non-equilibrium geometries: Dipole moment inversion and barriers to radical-radical association using XYG3 and XYGJ-OS

NASA Astrophysics Data System (ADS)

Hait, Diptarka; Head-Gordon, Martin

2018-05-01

Double hybrid (DH) density functionals are amongst the most accurate density functional approximations developed so far, largely due to the incorporation of correlation effects from unoccupied orbitals via second order perturbation theory (PT2). The xDH family of DH functionals calculate energy directly from orbitals optimized by a lower level approach like B3LYP, without self-consistent optimization. XYG3 and XYGJ-OS are two widely used xDH functionals that are known to be quite accurate at equilibrium geometries. Here, we show that the XYG3 and XYGJ-OS functionals can be ill behaved for stretched bonds well beyond the Coulson-Fischer point, predicting unphysical dipole moments and humps in potential energy curves for some simple systems like the hydrogen fluoride molecule. Numerical experiments and analysis show that these failures are not due to PT2. Instead, a large mismatch at stretched bond-lengths between the reference B3LYP orbitals and the optimized orbitals associated with the non-PT2 part of XYG3 leads to an unphysically large non-Hellman-Feynman contribution to first order properties like forces and electron densities.

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.

Nickel-Catalyzed Coupling Reactions of Alkyl Electrophiles, Including Unactivated Tertiary Halides, to Generate Carbon–Boron Bonds

PubMed Central

Dudnik, Alexander S.

2012-01-01

Through the use of a catalyst formed in situ from NiBr2•diglyme and a pybox ligand (both of which are commercially available), we have achieved our first examples of coupling reactions of unactivated tertiary alkyl electrophiles, as well as our first success with nickel-catalyzed couplings that generate bonds other than C–C bonds. Specifically, we have determined that this catalyst accomplishes Miyaura-type borylations of unactivated tertiary, secondary, and primary alkyl halides with diboron reagents to furnish alkylboronates, a family of compounds with substantial (and expanding) utility, under mild conditions; indeed, the umpolung borylation of a tertiary alkyl bromide can be achieved at a temperature as low as −10 °C. The method exhibits good functional-group compatibility and is regiospecific, both of which can be issues with traditional approaches to the synthesis of alkylboronates. In contrast to seemingly related nickel-catalyzed C–C bond-forming processes, tertiary halides are more reactive than secondary or primary halides in this nickel-catalyzed C–B bond-forming reaction; this divergence is particularly noteworthy in view of the likelihood that both transformations follow an inner-sphere electron-transfer pathway for oxidative addition. PMID:22668072

Theoretical and NMR conformational studies of β-proline oligopeptides with alternating chirality of pyrrolidine units

NASA Astrophysics Data System (ADS)

Mantsyzov, Alexey B.; Savelyev, Oleg Y.; Ivantcova, Polina M.; Bräse, Stefan; Kudryavtsev, Konstantin V.; Polshakov, Vladimir I.

2018-03-01

Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z/E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied β-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the β-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating β-proline pentapeptide, the presence of an E configuration for at least of one β-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of β-peptide bonds forming a wave-like extended structure.

Theoretical and NMR Conformational Studies of β-Proline Oligopeptides With Alternating Chirality of Pyrrolidine Units.

PubMed

Mantsyzov, Alexey B; Savelyev, Oleg Y; Ivantcova, Polina M; Bräse, Stefan; Kudryavtsev, Konstantin V; Polshakov, Vladimir I

2018-01-01

Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z / E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in their structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied β-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the β-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating β-proline pentapeptide, the presence of an E configuration for at least of one β-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of β-peptide bonds forming a wave-like extended structure.

Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase.

PubMed

Liu, Dongsheng; Cowburn, David

2016-01-01

The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk. Denaturation studies have shown that disulfide bond contributes significantly to the stability of SH2 domain, and crystal structures of the oxidized and C122S mutant showed minor conformational changes. We further investigated the binding of SH2 domain to a phosphorylated peptide from Csk-binding protein upon reduction and oxidation using both NMR and fluorescence approaches. This work employed NMR, X-ray cryptography, and other biophysical methods to study a disulfide bond in Csk SH2 domain. In addition, this work provides in-depth understanding of the structural dynamics of Csk SH2 domain.

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome.

PubMed

Song, Jiangning; Wang, Minglei; Burrage, Kevin

2006-07-21

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms.

Heterogeneous integration based on low-temperature bonding for advanced optoelectronic devices

NASA Astrophysics Data System (ADS)

Higurashi, Eiji

2018-04-01

Heterogeneous integration is an attractive approach to manufacturing future optoelectronic devices. Recent progress in low-temperature bonding techniques such as plasma activation bonding (PAB) and surface-activated bonding (SAB) enables a new approach to integrating dissimilar materials for a wide range of photonics applications. In this paper, low-temperature direct bonding and intermediate layer bonding techniques are focused, and their state-of-the-art applications in optoelectronic devices are reviewed. First, we describe the room-temperature direct bonding of Ge/Ge and Ge/Si wafers for photodetectors and of GaAs/SiC wafers for high-power semiconductor lasers. Then, we describe low-temperature intermediate layer bonding using Au and lead-free Sn-3.0Ag-0.5Cu solders for optical sensors and MEMS packaging.

Combined multifrequency EPR and DFT study of dangling bonds in a-Si:H

NASA Astrophysics Data System (ADS)

Fehr, M.; Schnegg, A.; Rech, B.; Lips, K.; Astakhov, O.; Finger, F.; Pfanner, G.; Freysoldt, C.; Neugebauer, J.; Bittl, R.; Teutloff, C.

2011-12-01

Multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy using S-, X-, Q-, and W-band frequencies (3.6, 9.7, 34, and 94 GHz, respectively) was employed to study paramagnetic coordination defects in undoped hydrogenated amorphous silicon (a-Si:H). The improved spectral resolution at high magnetic field reveals a rhombic splitting of the g tensor with the following principal values: gx=2.0079, gy=2.0061, and gz=2.0034, and shows pronounced g strain, i.e., the principal values are widely distributed. The multifrequency approach furthermore yields precise 29Si hyperfine data. Density functional theory (DFT) calculations on 26 computer-generated a-Si:H dangling-bond models yielded g values close to the experimental data but deviating hyperfine interaction values. We show that paramagnetic coordination defects in a-Si:H are more delocalized than computer-generated dangling-bond defects and discuss models to explain this discrepancy.

Activation of Carbon-Hydrogen and Hydrogen-Hydrogen Bonds by Copper-Nitrenes: A Comparison of Density Functional Theory with Single- and Multireference Correlation Consistent Composite Approaches.

PubMed

Tekarli, Sammer M; Williams, T Gavin; Cundari, Thomas R

2009-11-10

The kinetics and thermodynamics of copper-mediated nitrene insertion into C-H and H-H bonds (the former of methane) have been studied using several levels of theory: B3LYP/6-311++G(d,p), B97-1/cc-pVTZ, PBE1KCIS/cc-pVTZ, and ccCA (correlation consistent Composite Approach). The results show no significant difference among the DFT methods. All three DFT methods predict the ground state of the copper-nitrene model complex, L'Cu(NH), to be a triplet, while single reference ccCA predicts the singlet to be the ground state. The contributions to the total ccCA energy indicate that the singlet state is favored at the MP2/CBS level of theory, while electron correlation beyond this level (CCSD(T)) favors a triplet state, resulting in a close energetic balance between the two states. A multireference ccCA method is applied to the nitrene active species and supports the assignment of a singlet ground state. In general, the largest difference in the model reaction cycles between DFT and ccCA methods is for processes involving radicals and bond dissociation.

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

Bisti, F.; Stroppa, A.; Picozzi, S.

The electronic structure of Croconic Acid in the condensed phase has been studied by comparing core level and valence band x-ray photoelectron spectroscopy experiments and first principles density functional theory calculations using the Heyd-Scuseria-Ernzerhof screened hybrid functional and the GW approximation. By exploring the photoemission spectra for different deposition thicknesses, we show how the formation of the hydrogen bond network modifies the O 1s core level lineshape. Moreover, the valence band can be explained only if the intermolecular interactions are taken into account in the theoretical approach.

Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-03-01

Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

Electron transport in NH3/NO2 sensed buckled antimonene

NASA Astrophysics Data System (ADS)

Srivastava, Anurag; Khan, Md. Shahzad; Ahuja, Rajeev

2018-04-01

The structural and electronic properties of buckled antimonene have been analysed using density functional theory based ab-initio approach. Geometrical parameters in terms of bond length and bond angle are found close to the single ruffle mono-layer of rhombohedral antimony. Inter-frontier orbital analyses suggest localization of lone pair electrons at each atomic centre. Phonon dispersion along with high symmetry point of Brillouin zone does not signify any soft mode. With an electronic band gap of 1.8eV, the quasi-2D nano-surface has been further explored for NH3/NO2 molecules sensing and qualities of interaction between NH3/NO2 gas and antimonene scrutinized in terms of electronic charges transfer. A current-voltage characteristic has also been analysed, using Non Equilibrium Green's function (NEGF), for antimonene, in presence of incoming NH3/NO2 molecules.

Diversity of Chemical Bonding and Oxidation States in MS 4 Molecules of Group 8 Elements

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

Huang, Wei; Jiang, Ning; Schwarz, W. H. Eugen

The geometric and electronic ground-state structures of six MS 4 molecules (M = group-8 metals Fe, Ru, Os, Hs, Sm, and Pu) have been studied by using quantum-chemical density-functional and correlated wave-function approaches. The MS 4 species are compared to analogous MO 4 species recently investi-gated (Inorg. Chem. 2016, 55: 4616). Metal oxidation state (MOS) of high value VIII appears in low- spin singlet Td geometric species (Os,Hs)S 4 and (Ru,Os,Hs)O 4, whereas low MOS=II appears in high- spin septet D 2d species Fe(S 2) 2 and (slightly excited) metastable Fe(O 2) 2. The ground states of all other moleculesmore » have intermediate MOS values, containing S 2-, S 2 2-, S2 1- (and resp. O 2--, O 1-, O 2 2-, O 2 1-) ligands, bonded by ionic, covalent and correlative contributions.« less

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.

A non-JKL density matrix functional for intergeminal correlation between closed-shell geminals from analysis of natural orbital configuration interaction expansions

NASA Astrophysics Data System (ADS)

van Meer, R.; Gritsenko, O. V.; Baerends, E. J.

2018-03-01

Almost all functionals that are currently used in density matrix functional theory have been created by some a priori ansatz that generates approximations to the second-order reduced density matrix (2RDM). In this paper, a more consistent approach is used: we analyze the 2RDMs (in the natural orbital basis) of rather accurate multi-reference configuration interaction expansions for several small molecules (CH4, NH3, H2O, FH, and N2) and use the knowledge gained to generate new functionals. The analysis shows that a geminal-like structure is present in the 2RDMs, even though no geminal theory has been applied from the onset. It is also shown that the leading non-geminal dynamical correlation contributions are generated by a specific set of double excitations. The corresponding determinants give rise to non-JKL (non Coulomb/Exchange like) multipole-multipole dispersive attractive terms between geminals. Due to the proximity of the geminals, these dispersion terms are large and cannot be omitted, proving pure JKL functionals to be essentially deficient. A second correction emerges from the observation that the "normal" geminal-like exchange between geminals breaks down when one breaks multiple bonds. This problem can be fixed by doubling the exchange between bond broken geminals, effectively restoring the often physically correct high-spin configurations on the bond broken fragments. Both of these corrections have been added to the commonly used antisymmetrized product of strongly orthogonal geminals functional. The resulting non-JKL functional Extended Löwdin-Shull Dynamical-Multibond is capable of reproducing complete active space self-consistent field curves, in which one active orbital is used for each valence electron.

Natural bond orbital analysis in the ONETEP code: applications to large protein systems.

PubMed

Lee, Louis P; Cole, Daniel J; Payne, Mike C; Skylaris, Chris-Kriton

2013-03-05

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post-processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis-type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large-scale calculations with the ONETEP linear-scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long-range electronic effects from the entire system. We show that by transforming the Non-orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins--namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug-receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. Copyright © 2012 Wiley Periodicals, Inc.

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

Assessment of Orbital-Optimized MP2.5 for Thermochemistry and Kinetics: Dramatic Failures of Standard Perturbation Theory Approaches for Aromatic Bond Dissociation Energies and Barrier Heights of Radical Reactions.

PubMed

Soydaş, Emine; Bozkaya, Uğur

2015-04-14

An assessment of orbital-optimized MP2.5 (OMP2.5) [ Bozkaya, U.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 204105 ] for thermochemistry and kinetics is presented. The OMP2.5 method is applied to closed- and open-shell reaction energies, barrier heights, and aromatic bond dissociation energies. The performance of OMP2.5 is compared with that of the MP2, OMP2, MP2.5, MP3, OMP3, CCSD, and CCSD(T) methods. For most of the test sets, the OMP2.5 method performs better than MP2.5 and CCSD, and provides accurate results. For barrier heights of radical reactions and aromatic bond dissociation energies OMP2.5-MP2.5, OMP2-MP2, and OMP3-MP3 differences become obvious. Especially, for aromatic bond dissociation energies, standard perturbation theory (MP) approaches dramatically fail, providing mean absolute errors (MAEs) of 22.5 (MP2), 17.7 (MP2.5), and 12.8 (MP3) kcal mol(-1), while the MAE values of the orbital-optimized counterparts are 2.7, 2.4, and 2.4 kcal mol(-1), respectively. Hence, there are 5-8-folds reductions in errors when optimized orbitals are employed. Our results demonstrate that standard MP approaches dramatically fail when the reference wave function suffers from the spin-contamination problem. On the other hand, the OMP2.5 method can reduce spin-contamination in the unrestricted Hartree-Fock (UHF) initial guess orbitals. For overall evaluation, we conclude that the OMP2.5 method is very helpful not only for challenging open-shell systems and transition-states but also for closed-shell molecules. Hence, one may prefer OMP2.5 over MP2.5 and CCSD as an O(N(6)) method, where N is the number of basis functions, for thermochemistry and kinetics. The cost of the OMP2.5 method is comparable with that of CCSD for energy computations. However, for analytic gradient computations, the OMP2.5 method is only half as expensive as CCSD.

Interactively Applying the Variational Method to the Dihydrogen Molecule: Exploring Bonding and Antibonding

ERIC Educational Resources Information Center

Cruzeiro, Vinícius Wilian D.; Roitberg, Adrian; Polfer, Nicolas C.

2016-01-01

In this work we are going to present how an interactive platform can be used as a powerful tool to allow students to better explore a foundational problem in quantum chemistry: the application of the variational method to the dihydrogen molecule using simple Gaussian trial functions. The theoretical approach for the hydrogen atom is quite…

Phase transition analysis of V-shaped liquid crystal: Combined temperature-dependent FTIR and density functional theory approach

NASA Astrophysics Data System (ADS)

Singh, Swapnil; Singh, Harshita; Karthick, T.; Tandon, Poonam; Prasad, Veena

2018-01-01

Temperature-dependent Fourier transform infrared spectroscopy (FTIR) combined with density functional theory (DFT) is employed to study the mechanism of phase transitions of V-shaped bent-core liquid crystal. Since it has a large number of flexible bonds, one-dimensional potential energy scan (PES) was performed on the flexible bonds and predicted the most stable conformer I. A detailed analysis of vibrational normal modes of conformer I have been done on the basis of potential energy distribution. The good agreement between the calculated spectrum of conformer I and observed FTIR spectrum at room temperature validates our theoretical structure model. Furthermore, the prominent changes observed in the stretching vibrational bands of CH3/CH2, Cdbnd O, ring CC, ring CO, ring CH in-plane bending, and ring CH out-of-plane bending at Iso → nematic phase transition (at 155 °C) have been illustrated. However, the minor changes in the spectral features observed for the other phase transitions might be due to the shape or bulkiness of molecules. Combined FTIR and PES study beautifully explained the dynamics of the molecules, molecular realignment, H-bonding, and conformational changes at the phase transitions.

Hydrogen-bonded ring closing and opening of protonated methanol clusters H(+)(CH3OH)(n) (n = 4-8) with the inert gas tagging.

PubMed

Li, Ying-Cheng; Hamashima, Toru; Yamazaki, Ryoko; Kobayashi, Tomohiro; Suzuki, Yuta; Mizuse, Kenta; Fujii, Asuka; Kuo, Jer-Lai

2015-09-14

The preferential hydrogen bond (H-bond) structures of protonated methanol clusters, H(+)(MeOH)n, in the size range of n = 4-8, were studied by size-selective infrared (IR) spectroscopy in conjunction with density functional theory calculations. The IR spectra of bare clusters were compared with those with the inert gas tagging by Ar, Ne, and N2, and remarkable changes in the isomer distribution with the tagging were found for clusters with n≥ 5. The temperature dependence of the isomer distribution of the clusters was calculated by the quantum harmonic superposition approach. The observed spectral changes with the tagging were well interpreted by the fall of the cluster temperature with the tagging, which causes the transfer of the isomer distribution from the open and flexible H-bond network types to the closed and rigid ones. Anomalous isomer distribution with the tagging, which has been recently found for protonated water clusters, was also found for H(+)(MeOH)5. The origin of the anomaly was examined by the experiments on its carrier gas dependence.

Reliability of the pair-defect-sum approximation for the strength of valence-bond orbitals

PubMed Central

Pauling, Linus; Herman, Zelek S.; Kamb, Barclay J.

1982-01-01

The pair-defect-sum approximation to the bond strength of a hybrid orbital (angular wave functions only) is compared to the rigorous value as a function of bond angle for seven types of bonding situations, with between three and eight bond directions equivalent by geometrical symmetry operations and with only one independent bond angle. The approximation is seen to be an excellent one in all cases, and the results provide a rationale for the application of this approximation to a variety of problems. PMID:16593167

Programming the Assembly of Unnatural Materials with Nucleic Acids

NASA Astrophysics Data System (ADS)

Mirkin, Chad

Nature directs the assembly of enormously complex and highly functional materials through an encoded class of biomolecules, nucleic acids. The establishment of a similarly programmable code for the construction of synthetic, unnatural materials would allow researchers to impart functionality by precisely positioning all material components. Although it is exceedingly difficult to control the complex interactions between atomic and molecular species in such a manner, interactions between nanoscale components can be directed through the ligands attached to their surface. Our group has shown that nucleic acids can be used as highly programmable surface ligands to control the spacing and symmetry of nanoparticle building blocks in structurally sophisticated and functional materials. These nucleic acids function as programmable ``bonds'' between nanoparticle ``atoms,'' analogous to a nanoscale genetic code for assembling materials. The sequence and length tunability of nucleic acid bonds has allowed us to define a powerful set of design rules for the construction of nanoparticle superlattices with more than 30 unique lattice symmetries, tunable defect structures and interparticle spacings, and several well-defined crystal habits. Further, the nature of the nucleic acid bond enables an additional level of structural control: temporal regulation of dynamic material response to external biomolecular and chemical stimuli. This control allows for the reversible transformation between thermodynamic states with different crystal symmetries, particle stoichiometries, thermal stabilities, and interparticle spacings on demand. Notably, our unique genetic approach affords functional nanoparticle architectures that, among many other applications, can be used to systematically explore and manipulate optoelectronic material properties, such as tunable interparticle plasmonic interactions, microstructure-directed energy emission, and coupled plasmonic and photonic modes.

CO tip functionalization in subatomic resolution atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-10-01

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

CO tip functionalization in subatomic resolution atomic force microscopy

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

Kim, Minjung; Chelikowsky, James R.

2015-10-19

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

PubMed

Almonacid, Daniel E; Yera, Emmanuel R; Mitchell, John B O; Babbitt, Patricia C

2010-03-12

Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

PubMed Central

Almonacid, Daniel E.; Yera, Emmanuel R.; Mitchell, John B. O.; Babbitt, Patricia C.

2010-01-01

Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation. PMID:20300652

Automating Partial Period Bond Valuation with Excel's Day Counting Functions

ERIC Educational Resources Information Center

Vicknair, David; Spruell, James

2009-01-01

An Excel model for calculating the actual price of bonds under a 30 day/month, 360 day/year day counting assumption by nesting the DAYS360 function within the PV function is developed. When programmed into an Excel spreadsheet, the model can accommodate annual and semiannual payment bonds sold on or between interest dates using six fundamental…

The direct arylation of allylic sp3 C-H bonds via organic and photoredox catalysis

NASA Astrophysics Data System (ADS)

Cuthbertson, James D.; MacMillan, David W. C.

2015-03-01

The direct functionalization of unactivated sp3 C-H bonds is still one of the most challenging problems facing synthetic organic chemists. The appeal of such transformations derives from their capacity to facilitate the construction of complex organic molecules via the coupling of simple and otherwise inert building blocks, without introducing extraneous functional groups. Despite notable recent efforts, the establishment of general and mild strategies for the engagement of sp3 C-H bonds in C-C bond forming reactions has proved difficult. Within this context, the discovery of chemical transformations that are able to directly functionalize allylic methyl, methylene and methine carbons in a catalytic manner is a priority. Although protocols for direct oxidation and amination of allylic C-H bonds (that is, C-H bonds where an adjacent carbon is involved in a C = C bond) have become widely established, the engagement of allylic substrates in C-C bond forming reactions has thus far required the use of pre-functionalized coupling partners. In particular, the direct arylation of non-functionalized allylic systems would enable access to a series of known pharmacophores (molecular features responsible for a drug's action), though a general solution to this long-standing challenge remains elusive. Here we report the use of both photoredox and organic catalysis to accomplish a mild, broadly effective direct allylic C-H arylation. This C-C bond forming reaction readily accommodates a broad range of alkene and electron-deficient arene reactants, and has been used in the direct arylation of benzylic C-H bonds.

The direct arylation of allylic sp(3) C-H bonds via organic and photoredox catalysis.

PubMed

Cuthbertson, James D; MacMillan, David W C

2015-03-05

The direct functionalization of unactivated sp(3) C-H bonds is still one of the most challenging problems facing synthetic organic chemists. The appeal of such transformations derives from their capacity to facilitate the construction of complex organic molecules via the coupling of simple and otherwise inert building blocks, without introducing extraneous functional groups. Despite notable recent efforts, the establishment of general and mild strategies for the engagement of sp(3) C-H bonds in C-C bond forming reactions has proved difficult. Within this context, the discovery of chemical transformations that are able to directly functionalize allylic methyl, methylene and methine carbons in a catalytic manner is a priority. Although protocols for direct oxidation and amination of allylic C-H bonds (that is, C-H bonds where an adjacent carbon is involved in a C = C bond) have become widely established, the engagement of allylic substrates in C-C bond forming reactions has thus far required the use of pre-functionalized coupling partners. In particular, the direct arylation of non-functionalized allylic systems would enable access to a series of known pharmacophores (molecular features responsible for a drug's action), though a general solution to this long-standing challenge remains elusive. Here we report the use of both photoredox and organic catalysis to accomplish a mild, broadly effective direct allylic C-H arylation. This C-C bond forming reaction readily accommodates a broad range of alkene and electron-deficient arene reactants, and has been used in the direct arylation of benzylic C-H bonds.

Longitudinal Associations Between Parental Bonding, Parenting Stress, and Executive Functioning in Toddlerhood.

PubMed

de Cock, Evi S A; Henrichs, Jens; Klimstra, Theo A; Janneke B M Maas, A; Vreeswijk, Charlotte M J M; Meeus, Wim H J; van Bakel, Hedwig J A

2017-01-01

Early executive functioning is an important predictor for future development of children's cognitive skills and behavioral outcomes. Parenting behavior has proven to be a key environmental determinant of child executive functioning. However, the association of parental affect and cognitions directed to the child with child executive functioning has been understudied. Therefore, in the present study we examine the associations between parental bonding (i.e., the affective tie from parent to child), parenting stress, and child executive functioning. At 26 weeks of pregnancy, and at 6 months and 24 months postpartum the quality of the maternal (N = 335) and paternal (N = 261) bond with the infant was assessed. At 24 months, postnatal parenting stress and child executive functioning were measured by means of parent-report questionnaires. Results indicated that for both mothers and fathers feelings of bonding negatively predicted experienced parenting stress over time. In addition, for both parents a negative indirect effect of bonding on child executive functioning problems was found via experienced parenting stress. These findings indicate the importance of monitoring parents who experience a low level and quality of early parent-child bonding, as this makes them vulnerable to parenting stress, consequently putting their children at risk for developing executive functioning problems.

Social bonds affect anti-predator behaviour in a tolerant species of macaque, Macaca nigra.

PubMed

Micheletta, Jérôme; Waller, Bridget M; Panggur, Maria R; Neumann, Christof; Duboscq, Julie; Agil, Muhammad; Engelhardt, Antje

2012-10-07

Enduring positive social bonds between individuals are crucial for humans' health and well being. Similar bonds can be found in a wide range of taxa, revealing the evolutionary origins of humans' social bonds. Evidence suggests that these strong social bonds can function to buffer the negative effects of living in groups, but it is not known whether they also function to minimize predation risk. Here, we show that crested macaques (Macaca nigra) react more strongly to playbacks of recruitment alarm calls (i.e. calls signalling the presence of a predator and eliciting cooperative mobbing behaviour) if they were produced by an individual with whom they share a strong social bond. Dominance relationships between caller and listener had no effect on the reaction of the listener. Thus, strong social bonds may improve the coordination and efficiency of cooperative defence against predators, and therefore increase chances of survival. This result broadens our understanding of the evolution and function of social bonds by highlighting their importance in the anti-predator context.

Energy-Based Tissue Fusion for Sutureless Closure: Applications, Mechanisms, and Potential for Functional Recovery.

PubMed

Kramer, Eric A; Rentschler, Mark E

2018-06-04

As minimally invasive surgical techniques progress, the demand for efficient, reliable methods for vascular ligation and tissue closure becomes pronounced. The surgical advantages of energy-based vessel sealing exceed those of traditional, compression-based ligatures in procedures sensitive to duration, foreign bodies, and recovery time alike. Although the use of energy-based devices to seal or transect vasculature and connective tissue bundles is widespread, the breadth of heating strategies and energy dosimetry used across devices underscores an uncertainty as to the molecular nature of the sealing mechanism and induced tissue effect. Furthermore, energy-based techniques exhibit promise for the closure and functional repair of soft and connective tissues in the nervous, enteral, and dermal tissue domains. A constitutive theory of molecular bonding forces that arise in response to supraphysiological temperatures is required in order to optimize and progress the use of energy-based tissue fusion. While rapid tissue bonding has been suggested to arise from dehydration, dipole interactions, molecular cross-links, or the coagulation of cellular proteins, long-term functional tissue repair across fusion boundaries requires that the reaction to thermal damage be tailored to catalyze the onset of biological healing and remodeling. In this review, we compile and contrast findings from published thermal fusion research in an effort to encourage a molecular approach to characterization of the prevalent and promising energy-based tissue bond.

NMR Investigations of Noncovalent Carbon Tetrel Bonds. Computational Assessment and Initial Experimental Observation.

PubMed

Southern, Scott A; Bryce, David L

2015-12-10

Group IV tetrel elements may act as tetrel bond donors, whereby a region of positive electrostatic potential (σ-hole) interacts with a Lewis base. The results of calculations of NMR parameters are reported for a series of model compounds exhibiting tetrel bonding from a methyl carbon to the oxygen or nitrogen atoms in various functional groups. The (13)C chemical shift (δiso) and the (1c)J((13)C,Y) coupling (Y = (17)O, (15)N) across the tetrel bond are recorded as a function of geometry. The sensitivity of the NMR parameters to the noncovalent interaction is demonstrated via an increase in δiso and in |(1c)J((13)C,Y)| as the tetrel bond shortens. Gauge-including projector-augmented wave density functional theory (DFT) calculations of δiso are reported for crystals that exhibit tetrel bonding in the solid state. Experimental δiso values for solid sarcosine and its tetrel-bonded salts corroborate the computational findings. This work offers new insights into tetrel bonding and facilitates the incorporation of tetrel bonds as restraints in NMR crystallographic structure refinement.

Calculation of nuclear spin-spin coupling constants using frozen density embedding

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

Götz, Andreas W., E-mail: agoetz@sdsc.edu; Autschbach, Jochen; Visscher, Lucas, E-mail: visscher@chem.vu.nl

2014-03-14

We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects inmore » the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between {sup 199}Hg and {sup 13}C upon coordination of dimethylsulfoxide solvent molecules.« less

Multi-wafer bonding technology for the integration of a micromachined Mirau interferometer

NASA Astrophysics Data System (ADS)

Wang, Wei-Shan; Lullin, Justine; Froemel, Joerg; Wiemer, Maik; Bargiel, Sylwester; Passilly, Nicolas; Gorecki, Christophe; Gessner, Thomas

2015-02-01

The paper presents the multi-wafer bonding technology as well as the integration of electrical connection to the zscanner wafer of the micromachined array-type Mirau interferometer. A Mirau interferometer, which is a key-component of optical coherence tomography (OCT) microsystem, consists of a microlens doublet, a MOEMS Z-scanner, a focusadjustment spacer and a beam splitter plate. For the integration of this MOEMS device heterogeneous bonding of Si, glass and SOI wafers is necessary. Previously, most of the existing methods for multilayer wafer bonding require annealing at high temperature, i.e., 1100°C. To be compatible with MEMS devices, bonding of different material stacks at temperatures lower than 400°C has also been investigated. However, if more components are involved, it becomes less effective due to the alignment accuracy or degradation of surface quality of the not-bonded side after each bonding operation. The proposed technology focuses on 3D integration of heterogeneous building blocks, where the assembly process is compatible with the materials of each wafer stack and with position accuracy which fits optical requirement. A demonstrator with up to 5 wafers bonded lower than 400°C is presented and bond interfaces are evaluated. To avoid the complexity of through wafer vias, a design which creates electrical connections along vertical direction by mounting a wafer stack on a flip chip PCB is proposed. The approach, which adopts vertically-stacked wafers along with electrical connection functionality, provides not only a space-effective integration of MOEMS device but also a design where the Mirau stack can be further integrated with other components of the OCT microsystem easily.

Development of simulation approach for two-dimensional chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface

NASA Astrophysics Data System (ADS)

Qin, Yuan; Yao, Man; Hao, Ce; Wan, Lijun; Wang, Yunhe; Chen, Ting; Wang, Dong; Wang, Xudong; Chen, Yonggang

2017-09-01

Two-dimensional (2D) chiral self-assembly system of 5-(benzyloxy)-isophthalic acid derivative/(S)-(+)-2-octanol/highly oriented pyrolytic graphite was studied. A combined density functional theory/molecular mechanics/molecular dynamics (DFT/MM/MD) approach for system of 2D chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface was thus proposed. Structural models of the chiral assembly were built on the basis of scanning tunneling microscopy (STM) images and simplified for DFT geometry optimization. Merck Molecular Force Field (MMFF) was singled out as the suitable force field by comparing the optimized configurations of MM and DFT. MM and MD simulations for hexagonal unit model which better represented the 2D assemble network were then preformed with MMFF. The adhesion energy, evolution of self-assembly process and characteristic parameters of hydrogen bond were obtained and analyzed. According to the above simulation, the stabilities of the clockwise and counterclockwise enantiomorphous networks were evaluated. The calculational results were supported by STM observations and the feasibility of the simulation method was confirmed by two other systems in the presence of chiral co-absorbers (R)-(-)-2-octanol and achiral co-absorbers 1-octanol. This theoretical simulation method assesses the stability trend of 2D enantiomorphous assemblies with atomic scale and can be applied to the similar hydrogen bond driven 2D chirality of molecular self-assembly system.

Childhood bereavement: The role of the surviving parent and the continuing bond with the deceased.

PubMed

Karydi, Evangelia

2018-08-01

This study investigated the relationship between the role of the surviving parent in the child's grieving process, the continuing bond with the deceased parent and biopsychosocial functioning and active grief in adulthood. A survey of 135 adults, parentally bereaved in childhood, indicated that the surviving parent's role in facilitating the grieving process promoted a positive continuing bond with the deceased in childhood as well as general functioning in adulthood. The continuing bond with the deceased had a weak association with both better general functioning and relational active grief.

Methodological Issues in Meta-Analyzing Standard Deviations: Comment on Bond and DePaulo (2008)

ERIC Educational Resources Information Center

Pigott, Therese D.; Wu, Meng-Jia

2008-01-01

In this comment on C. F. Bond and B. M. DePaulo, the authors raise methodological concerns about the approach used to analyze the data. The authors suggest further refinement of the procedures used, and they compare the approach taken by Bond and DePaulo with standard methods for meta-analysis. (Contains 1 table and 2 figures.)

Force Field Model of Periodic Trends in Biomolecular Halogen Bonds

PubMed Central

Scholfield, Matthew R.; Ford, Melissa Coates; Vander Zanden, Crystal M.; Billman, M. Marie; Ho, P. Shing; Rappé, Anthony K.

2016-01-01

The study of the noncovalent interaction now defined as a halogen bond (X-bond) has become one of the fastest growing areas in experimental and theoretical chemistry—its applications as a design tool are highly extensive. The significance of the interaction in biology has only recently been recognized, but has now become important in medicinal chemistry. We had previously derived a set of empirical potential energy functions to model the structure-energy relationships for bromines in biomolecular X-bonds (BXBs). Here, we have extended this force field for BXBs (ffBXB) to the halogens (Cl, Br, and I) that are commonly seen to form stable X-bonds. The ffBXB calculated energies show a remarkable one-to-one linear relationship to explicit BXB energies determined from an experimental DNA junction system, thereby validating the approach and the model. The resulting parameters allow us to interpret the stabilizing effects of BXBs in terms of well-defined physical properties of the halogen atoms, including their size, shape, and charge, showing periodic trends that are predictable along the Group VII column of elements. Consequently, we have established the ffBXB as accurate computational tool that can be applied to, for example, for the design of new therapeutic compounds against clinically important targets and new biomolecular based materials. PMID:25338128

Regioselective oxyalkylation of vinylarenes catalyzed by diatomite-supported manganese oxide nanoparticles.

PubMed

Sun, Huayin; Zhang, Yonghui; Guo, Fengfeng; Zha, Zhenggen; Wang, Zhiyong

2012-04-06

A regioselective oxyalkylation reaction of vinylarenes with cyclic ethers was developed under the catalysis of a new heterogeneous catalyst, the diatomite-supported Mn(3)O(4) nanoparticles (SMONP-1). The use of this heterogeneous catalyst provided a novel approach for the synthesis of α-carbonyled β-alkylated aryl derivatives via a sp(3) C-H bond functionalization under mild aerobic conditions.

The anchoring function: parental authority and the parent-child bond.

PubMed

Omer, Haim; Steinmetz, Sarit G; Carthy, Tal; von Schlippe, Arist

2013-06-01

Descriptions of parental authority and of the formation of a secure parent-child bond have remained unconnected in conceptualizations about parenting and child development. The parental anchoring function is here presented as an integrative metaphor for the two fields. Parents who fulfill an anchoring function offer a secure relational frame for the child, while also manifesting a stabilizing and legitimate kind of authority. The anchoring function enriches the two fields by: (1) adding a dimension of authority to the acknowledged functions of the safe haven and the secure base that are seen as core to a secure parent-child bond, and (2) adding considerations about the parent-child bond to Baumrind's classical description of authoritative parenting. © FPI, Inc.

Ab-initio adsorption study of chitosan on functionalized graphene: critical role of van der Waals interactions.

PubMed

Rahman, R; Mazumdar, D

2012-03-01

We investigate the adsorption process of an organic biomolecule (chitosan) on epoxy-functionalized graphene using ab-initio density functional methods incorporating van-der-waals (vdW) interactions. The role of London dispersion force on the cohesive energy and conformal preference of the molecule is quantitatively elucidated. Functionalizing graphene with epoxy leads to weak hydrogen-bond interactions with chitosan. Binding energy values increase by over an order of magnitude after including vdW corrections, implying that dispersive interactions dominate the physisorption process. Conformal study show binding upto 30 kcal/mol when the molecule is oriented with the hydroxyl group approaching the functionalized graphene. Our study advances the promise of functionalized graphene for a variety of applications.

Generating carbyne equivalents with photoredox catalysis

NASA Astrophysics Data System (ADS)

Wang, Zhaofeng; Herraiz, Ana G.; Del Hoyo, Ana M.; Suero, Marcos G.

2018-02-01

Carbon has the unique ability to bind four atoms and form stable tetravalent structures that are prevalent in nature. The lack of one or two valences leads to a set of species—carbocations, carbanions, radicals and carbenes—that is fundamental to our understanding of chemical reactivity. In contrast, the carbyne—a monovalent carbon with three non-bonded electrons—is a relatively unexplored reactive intermediate; the design of reactions involving a carbyne is limited by challenges associated with controlling its extreme reactivity and the lack of efficient sources. Given the innate ability of carbynes to form three new covalent bonds sequentially, we anticipated that a catalytic method of generating carbynes or related stabilized species would allow what we term an ‘assembly point’ disconnection approach for the construction of chiral centres. Here we describe a catalytic strategy that generates diazomethyl radicals as direct equivalents of carbyne species using visible-light photoredox catalysis. The ability of these carbyne equivalents to induce site-selective carbon-hydrogen bond cleavage in aromatic rings enables a useful diazomethylation reaction, which underpins sequencing control for the late-stage assembly-point functionalization of medically relevant agents. Our strategy provides an efficient route to libraries of potentially bioactive molecules through the installation of tailored chiral centres at carbon-hydrogen bonds, while complementing current translational late-stage functionalization processes. Furthermore, we exploit the dual radical and carbene character of the generated carbyne equivalent in the direct transformation of abundant chemical feedstocks into valuable chiral molecules.

The nature of the interaction of dimethylselenide with IIIA group element compounds.

PubMed

Madzhidov, Timur I; Chmutova, Galina A

2013-05-16

The first systematic theoretical study of the nature of intermolecular bonding of dimethylselenide as donor and IIIA group element halides as acceptors was made with the help of the approach of Quantum Theory of Atoms in Molecules. Density Functional Theory with "old" Sapporo triple-ζ basis sets was used to calculate geometry, thermodynamics, and wave function of Me2Se···AX3 complexes. The analysis of the electron density distribution and the Laplacian of the electron density allowed us to reveal and explain the tendencies in the influence of the central atom (A = B, Al, Ga, In) and halogen (X = F, Cl, Br, I) on the nature of Se···A bonding. Significant changes in properties of the selenium lone pair upon complexation were described by means of the analysis of the Laplacian of the charge density. Charge transfer characteristics and the contributions to it from electron localization and delocalization were analyzed in terms of localization and delocalization indexes. Common features of the complexation and differences in the nature of bonding were revealed. Performed analysis evidenced that gallium and indium halide complexes can be attributed to charge transfer-driven complexes; aluminum halides complexes seem to be mainly of an electrostatic nature. The nature of bonding in different boron halides essentially varies; these complexes are stabilized mainly by covalent Se···B interaction. In all the complexes under study covalence of the Se···A interaction is rather high.

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.

Synthesis of hybrid cellulose nanocomposite bonded with dopamine SiO2/TiO2 and its antimicrobial activity

NASA Astrophysics Data System (ADS)

Ramesh, Sivalingam; Kim, Gwang-Hoon; Kim, Jaehwan; Kim, Joo-Hyung

2015-04-01

Organic-inorganic hybrid material based cellulose was synthesized by the sol-gel approach. The explosion of activity in this area in the past decade has made tremendous progress in industry or academic both fundamental understanding of sol-gel process and applications of new functionalized hybrid materials. In this present research work, we focused on cellulose-dopamine functionalized SiO2/TiO2 hybrid nanocomposite by sol-gel process. The cellulose-dopamine hybrid nanocomposite was synthesized via γ-aminopropyltriethoxysilane (γ-APTES) coupling agent by in-situ sol-gel process. The chemical structure of cellulose-amine functionalized dopamine bonding to cellulose structure with covalent cross linking hybrids was confirmed by FTIR spectral analysis. The morphological analysis of cellulose-dopamine nanoSiO2/TiO2 hybrid nanocomposite materials was characterized by XRD, SEM and TEM. From this different analysis results indicate that the optical transparency, thermal stability, control morphology of cellulose-dopamine-SiO2/TiO2 hybrid nanocomposite. Furthermore cellulose-dopamine-SiO2/TiO2 hybrid nanocomposite was tested against pathogenic bacteria for antimicrobial activity.

Self‐Assembled Graphene‐Based Architectures and Their Applications

PubMed Central

Yuan, Zhongke; Xiao, Xiaofen; Li, Jing; Zhao, Zhe

2017-01-01

Abstract Due to unique planar structures and remarkable thermal, electronic, and mechanical properties, chemically modified graphenes (CMGs) such as graphene oxides, reduced graphene oxides, and the related derivatives are recognized as the attractive building blocks for “bottom‐up” nanotechnology, while self‐assembly of CMGs has emerged as one of the most promising approaches to construct advanced functional materials/systems based on graphene. By virtue of a variety of noncovalent forces like hydrogen bonding, van der Waals interaction, metal‐to‐ligand bonds, electrostatic attraction, hydrophobic–hydrophilic interactions, and π–π interactions, the CMGs bearing various functional groups are highly desirable for the assemblies with themselves and a variety of organic and/or inorganic species which can yield various hierarchical nanostructures and macroscopic composites endowed with unique structures, properties, and functions for widespread technological applications such as electronics, optoelectronics, electrocatalysis/photocatalysis, environment, and energy storage and conversion. In this review, significant recent advances concerning the self‐assembly of CMGs are summarized, and the broad applications of self‐assembled graphene‐based materials as well as some future opportunities and challenges in this vibrant area are elucidated. PMID:29619311

New Methods of Esterification of Nanodiamonds in Fighting Breast Cancer-A Density Functional Theory Approach.

PubMed

Landeros-Martinez, Linda-Lucila; Glossman-Mitnik, Daniel; Orrantia-Borunda, Erasmo; Flores-Holguín, Norma

2017-10-19

The use of nanodiamonds as anticancer drug delivery vehicles has received much attention in recent years. In this theoretical paper, we propose using different esterification methods for nanodiamonds. The monomers proposed are 2-hydroxypropanal, polyethylene glycol, and polyglicolic acid. Specifically, the hydrogen bonds, infrared (IR) spectra, molecular polar surface area, and reactivity parameters are analyzed. The monomers proposed for use in esterification follow Lipinski's rule of five, meaning permeability is good, they have good permeation, and their bioactivity is high. The results show that the complex formed between tamoxifen and nanodiamond esterified with polyglicolic acid presents the greatest number of hydrogen bonds and a good amount of molecular polar surface area. Calculations concerning the esterified nanodiamond and reactivity parameters were performed using Density Functional Theory with the M06 functional and the basis set 6-31G (d); for the esterified nanodiamond-Tamoxifen complexes, the semi-empirical method PM6 was used. The solvent effect has been taken into account by using implicit modelling and the conductor-like polarizable continuum model.

A new quasi-relativistic approach for density functional theory based on the normalized elimination of the small component

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2002-01-01

A recently developed variationally stable quasi-relativistic method, which is based on the low-order approximation to the method of normalized elimination of the small component, was incorporated into density functional theory (DFT). The new method was tested for diatomic molecules involving Ag, Cd, Au, and Hg by calculating equilibrium bond lengths, vibrational frequencies, and dissociation energies. The method is easy to implement into standard quantum chemical programs and leads to accurate results for the benchmark systems studied.

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

Social bonds affect anti-predator behaviour in a tolerant species of macaque, Macaca nigra

PubMed Central

Micheletta, Jérôme; Waller, Bridget M.; Panggur, Maria R.; Neumann, Christof; Duboscq, Julie; Agil, Muhammad; Engelhardt, Antje

2012-01-01

Enduring positive social bonds between individuals are crucial for humans' health and well being. Similar bonds can be found in a wide range of taxa, revealing the evolutionary origins of humans' social bonds. Evidence suggests that these strong social bonds can function to buffer the negative effects of living in groups, but it is not known whether they also function to minimize predation risk. Here, we show that crested macaques (Macaca nigra) react more strongly to playbacks of recruitment alarm calls (i.e. calls signalling the presence of a predator and eliciting cooperative mobbing behaviour) if they were produced by an individual with whom they share a strong social bond. Dominance relationships between caller and listener had no effect on the reaction of the listener. Thus, strong social bonds may improve the coordination and efficiency of cooperative defence against predators, and therefore increase chances of survival. This result broadens our understanding of the evolution and function of social bonds by highlighting their importance in the anti-predator context. PMID:22859593

Homologation chemistry with nucleophilic α-substituted organometallic reagents: chemocontrol, new concepts and (solved) challenges.

PubMed

Castoldi, Laura; Monticelli, Serena; Senatore, Raffaele; Ielo, Laura; Pace, Vittorio

2018-05-31

The transfer of a reactive nucleophilic CH2X unit into a preformed bond enables the introduction of a fragment featuring the exact and desired degree of functionalization through a single synthetic operation. The instability of metallated α-organometallic species often poses serious questions regarding the practicability of using this conceptually intuitive and simple approach for forming C-C or C-heteroatom bonds. A deep understanding of processes regulating the formation of these nucleophiles is a precious source of inspiration not only for successfully applying theoretically feasible transformations (i.e. determining how to employ a given reagent), but also for designing new reactions which ultimately lead to the introduction of molecular complexity via short experimental sequences.

Charge transfer interactions and nonlinear optical properties of push pull chromophore benzaldehyde phenylhydrazone: A vibrational approach

NASA Astrophysics Data System (ADS)

Ravikumar, C.; Joe, I. Hubert; Jayakumar, V. S.

2008-07-01

FT Raman and IR spectra of the crystallized nonlinear optic (NLO) molecule, benzaldehyde phenylhydrazone (BPH) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of BPH have been investigated with the help of B3LYP density functional theory (DFT) method. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). From the optimized geometry, the decrease in C-N bond length indicates the electron delocalization over the region of the molecule. The vibrational analysis confirm the charge transfer interaction between the phenyl rings through ≻Cdbnd N-N≺ skeleton.

Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory.

PubMed

Amin, Elizabeth A; Truhlar, Donald G

2008-01-01

We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn-ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.

Palladium-catalysed anti-Markovnikov selective oxidative amination

NASA Astrophysics Data System (ADS)

Kohler, Daniel G.; Gockel, Samuel N.; Kennemur, Jennifer L.; Waller, Peter J.; Hull, Kami L.

2018-03-01

In recent years, the synthesis of amines and other nitrogen-containing motifs has been a major area of research in organic chemistry because they are widely represented in biologically active molecules. Current strategies rely on a multistep approach and require one reactant to be activated prior to the carbon-nitrogen bond formation. This leads to a reaction inefficiency and functional group intolerance. As such, a general approach to the synthesis of nitrogen-containing compounds from readily available and benign starting materials is highly desirable. Here we present a palladium-catalysed oxidative amination reaction in which the addition of the nitrogen occurs at the less-substituted carbon of a double bond, in what is known as anti-Markovnikov selectivity. Alkenes are shown to react with imides in the presence of a palladate catalyst to generate the terminal imide through trans-aminopalladation. Subsequently, olefin isomerization occurs to afford the thermodynamically favoured products. Both the scope of the transformation and mechanistic investigations are reported.

A Vibrational Spectral Maker for Probing the Hydrogen-Bonding Status of Protonated Asp and Glu Residues

PubMed Central

Nie, Beining; Stutzman, Jerrod; Xie, Aihua

2005-01-01

Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. We report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated Asp or Glu residues in proteins. Ab initio computational studies were performed on hydrogen-bonding interactions of a COOH group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function theory. For hydrogen-bonding interactions with polar side-chain groups, our results show a strong correlation between the C=O stretching frequency and the hydrogen bond number of a COOH group: ∼1759–1776 cm−1 for zero, ∼1733–1749 cm−1 for one, and 1703–1710 cm−1 for two hydrogen bonds. Experimental evidence for this correlation will be discussed. In addition, we show an approximate linear correlation between the C=O stretching frequency and the hydrogen-bond strength. We propose that a two-dimensional infrared spectroscopy, C=O stretching versus O-H stretching, may be employed to identify the specific type of hydrogen-bonding interaction. This vibrational spectral marker for hydrogen-bonding interaction is expected to enhance the power of time-resolved Fourier transform infrared spectroscopy for structural characterization of functionally important intermediates of proteins. PMID:15653739

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Formation of conjugated delta8,delta10-double bonds by delta12-oleic-acid desaturase-related enzymes: biosynthetic origin of calendic acid.

PubMed

Cahoon, E B; Ripp, K G; Hall, S E; Kinney, A J

2001-01-26

Divergent forms of the plant Delta(12)-oleic-acid desaturase (FAD2) have previously been shown to catalyze the formation of acetylenic bonds, epoxy groups, and conjugated Delta(11),Delta(13)-double bonds by modification of an existing Delta(12)-double bond in C(18) fatty acids. Here, we report a class of FAD2-related enzymes that modifies a Delta(9)-double bond to produce the conjugated trans-Delta(8),trans-Delta(10)-double bonds found in calendic acid (18:3Delta(8trans,10trans,12cis)), the major component of the seed oil of Calendula officinalis. Using an expressed sequence tag approach, cDNAs for two closely related FAD2-like enzymes, designated CoFADX-1 and CoFADX-2, were identified from a C. officinalis developing seed cDNA library. The deduced amino acid sequences of these polypeptides share 40-50% identity with those of other FAD2 and FAD2-related enzymes. Expression of either CoFADX-1 or CoFADX-2 in somatic soybean embryos resulted in the production of calendic acid. In embryos expressing CoFADX-2, calendic acid accumulated to as high as 22% (w/w) of the total fatty acids. In addition, expression of CoFADX-1 and CoFADX-2 in Saccharomyces cerevisiae was accompanied by calendic acid accumulation when induced cells were supplied exogenous linoleic acid (18:2Delta(9cis,12cis)). These results are thus consistent with a route of calendic acid synthesis involving modification of the Delta(9)-double bond of linoleic acid. Regiospecificity for Delta(9)-double bonds is unprecedented among FAD2-related enzymes and further expands the functional diversity found in this family of enzymes.

Chemical synthesis of La1 isolated from the venom of the scorpion Liocheles australasiae and determination of its disulfide bonding pattern.

PubMed

Nagao, Junya; Miyashita, Masahiro; Nakagawa, Yoshiaki; Miyagawa, Hisashi

2015-08-01

La1 is a 73-residue cysteine-rich peptide isolated from the scorpion Liocheles australasiae venom. Although La1 is the most abundant peptide in the venom, its biological function remains unknown. Here, we describe a method for efficient chemical synthesis of La1 using the native chemical ligation (NCL) strategy, in which three peptide components of less than 40 residues were sequentially ligated. The peptide thioester necessary for NCL was synthesized using an aromatic N-acylurea approach with Fmoc-SPPS. After completion of sequential NCL, disulfide bond formation was carried out using a dialysis method, in which the linear peptide dissolved in an acidic solution was dialyzed against a slightly alkaline buffer to obtain correctly folded La1. Next, we determined the disulfide bonding pattern of La1. Enzymatic and chemical digests of La1 without reduction of disulfide bonds were analyzed by liquid chromatography/mass spectrometry (LC/MS), which revealed two of four disulfide bond linkages. The remaining two linkages were assigned based on MS/MS analysis of a peptide fragment containing two disulfide bonds. Consequently, the disulfide bonding pattern of La1 was found to be similar to that of a von Willebrand factor type C (VWC) domain. To our knowledge, this is the first report of the experimental determination of the disulfide bonding pattern of peptides having a single VWC domain as well as their chemical synthesis. La1 synthesized in this study will be useful for investigation of its biological role in the venom. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction.

PubMed

Gawthrop, Peter J

2017-04-01

Engineering systems modeling and analysis based on the bond graph approach has been applied to biomolecular systems. In this context, the notion of a Faraday-equivalent chemical potential is introduced which allows chemical potential to be expressed in an analogous manner to electrical volts thus allowing engineering intuition to be applied to biomolecular systems. Redox reactions, and their representation by half-reactions, are key components of biological systems which involve both electrical and chemical domains. A bond graph interpretation of redox reactions is given which combines bond graphs with the Faraday-equivalent chemical potential. This approach is particularly relevant when the biomolecular system implements chemoelectrical transduction - for example chemiosmosis within the key metabolic pathway of mitochondria: oxidative phosphorylation. An alternative way of implementing computational modularity using bond graphs is introduced and used to give a physically based model of the mitochondrial electron transport chain To illustrate the overall approach, this model is analyzed using the Faraday-equivalent chemical potential approach and engineering intuition is used to guide affinity equalisation: a energy based analysis of the mitochondrial electron transport chain.

An equivalent dipole analysis of PZT ceramics and lead-free piezoelectric single crystals

NASA Astrophysics Data System (ADS)

Bell, Andrew J.

2016-04-01

The recently proposed Equivalent Dipole Model for describing the electromechanical properties of ionic solids in terms of 3 ions and 2 bonds has been applied to PZT ceramics and lead-free single crystal piezoelectric materials, providing analysis in terms of an effective ionic charge and the asymmetry of the interatomic force constants. For PZT it is shown that, as a function of composition across the morphotropic phase boundary, the dominant bond compliance peaks at 52% ZrO2. The stiffer of the two bonds shows little composition dependence with no anomaly at the phase boundary. The effective charge has a maximum value at 50% ZrO2, decreasing across the phase boundary region, but becoming constant in the rhombohedral phase. The single crystals confirm that both the asymmetry in the force constants and the magnitude of effective charge are equally important in determining the values of the piezoelectric charge coefficient and the electromechanical coupling coefficient. Both are apparently temperature dependent, increasing markedly on approaching the Curie temperature.

How Early Bonding, Depression, Illicit Drug Use, and Perceived Support Work Together to Influence Drug-Dependent Mothers’ Caregiving

PubMed Central

Suchman, Nancy E.; McMahon, Thomas J.; Slade, Arietta; Luthar, Suniya S.

2007-01-01

In this study, the authors used an attachment framework to examine how drug-dependent mothers’ early bonding experience, depression, illicit drug use, and perceived support work together to influence the family environment. The authors hypothesized that (a) depression and drug use function as proxies for a stronger risk factor, the perceived absence of support available in everyday life, and (b) associations between mothers’ early bonding experience and family environment are mediated by perceptions of support and nurture available in everyday life. The authors used a “building block” analytic approach and data collected from 125 mothers enrolled in methadone maintenance to test hypotheses. Both hypotheses were confirmed for 1 outcome, family adaptability. For the 2nd outcome, family cohesion, only perceived support was a significant predictor. Although preliminary, the findings suggest that perceptions of relationships in everyday life play a critical role in the etiology of drug-dependent mothers’ parenting. PMID:16060738

DFT study of the adsorption of 3-chloro-2-hydroxypropyl trimethylammonium chloride on montmorillonite surfaces in solution

NASA Astrophysics Data System (ADS)

Yang, Zongyi; Liu, Wenli; Zhang, He; Jiang, Xinli; Min, Fanfei

2018-04-01

The study of the adsorption mechanism of 3-chloro-2-hydroxypropyl trimethylammonium chloride (CHPTA), which acts as an effective clay minerals hydration inhibitor, can provide an effective approach for the design of novel high-performance inhibitors with favorable molecular structures. Density functional theory (DFT) calculations were performed to investigate the adsorption mechanism of CHPTA on dry and hydrated montmorillonite (MMT) surfaces. The interactions between CHPTA, H2O, and MMT were systematically analyzed. It was found that CHPTA was mainly adsorbed on MMT by hydrogen bonds and especially electrostatic force and that the presence of Na ions favors the adsorption of CHPTA on the Na-(001) surface. In the presence of water molecules, the adsorption of CHPTA was promoted by H2O, which exhibited a cooperative adsorption effect by enhancing the MMT-CHPTA electrostatic force and by forming more hydrogen bonds and Hsbnd Cl bonds among CHPTA, H2O and MMT.

Structural characteristics and harmonic vibrational analysis of the stable conformer of 2,3-epoxypropanol by quantum chemical methods.

PubMed

Arjunan, V; Rani, T; Santhanam, R; Mohan, S

2012-10-01

The FT-IR and FT-Raman spectra of H bond inner conformer of 2,3-epoxypropanol have been recorded in the regions 3700-400 and 3700-100 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The normal coordinate analysis was carried out to confirm the precision of the assignments. The structure of the conformers H bond inner and H bond outer1 were optimised and the structural characteristics were determined by density functional theory (DFT) using B3LYP and MP2 methods with 6-31G** and 6-311++G** basis sets. The vibrational frequencies were calculated in all these methods and were compared with the experimental frequencies which yield good agreement between observed and calculated frequencies. The electronic properties HOMO and LUMO energies were measured by time-dependent TD-DFT approach. Copyright © 2012 Elsevier B.V. All rights reserved.

Dynamic covalent chemistry of bisimines at the solid/liquid interface monitored by scanning tunnelling microscopy.

PubMed

Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo

2014-11-01

Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.

Identification of phases, symmetries and defects through local crystallography

DOE PAGES

Belianinov, Alex; He, Qian; Kravchenko, Mikhail; ...

2015-07-20

Here we report that advances in electron and probe microscopies allow 10 pm or higher precision in measurements of atomic positions. This level of fidelity is sufficient to correlate the length (and hence energy) of bonds, as well as bond angles to functional properties of materials. Traditionally, this relied on mapping locally measured parameters to macroscopic variables, for example, average unit cell. This description effectively ignores the information contained in the microscopic degrees of freedom available in a high-resolution image. Here we introduce an approach for local analysis of material structure based on statistical analysis of individual atomic neighbourhoods. Clusteringmore » and multivariate algorithms such as principal component analysis explore the connectivity of lattice and bond structure, as well as identify minute structural distortions, thus allowing for chemical description and identification of phases. This analysis lays the framework for building image genomes and structure–property libraries, based on conjoining structural and spectral realms through local atomic behaviour.« less

Ab initio computational study of –N-C and –O-C bonding formation : functional group modification reaction based chitosan

NASA Astrophysics Data System (ADS)

Siahaan, P.; Salimah, S. N. M.; Sipangkar, M. J.; Hudiyanti, D.; Djunaidi, M. C.; Laksitorini, M. D.

2018-04-01

Chitosan application in pharmaceutics and cosmeceutics industries is limited by its solubility issue. Modification of -NH2 and -OH fuctional groups of chitosan by adding carboxyl group has been shown to improve its solubility and application. Attempt to synthesize carboxymethyl chitosan (CMC) from monocloroacetic acid (MCAA) has been done prior this report. However no information is available wether –OH (-O-C bonding formation) or -NH2 (-N-C bonding formation) is the preference for - CH2COOH to attach. In the current study, the reaction mechanism between chitosan and MCAA reactants into carboxymethyl chitosan (CMC) was examined by computational approach. Dimer from of chitosan used as a molecular model in calculation All the molecular structure involved in the reaction mechanism was optimized by ab initio computational on the theory and basis set HF/6-31G(d,p). The results showed that the - N-C bonding formation via SN2 than the -O-C bonding formation via SN2 which have activation energy 469.437 kJ/mol and 533.219 kJ/mol respectively. However, the -O-C bonding formation more spontaneous than the -N-C bonding formation because ΔG the formation of O-CMC-2 reaction is more negative than ΔG of formation N-CMC-2 reaction is -4.353 kJ/mol and -1.095 kJ/mol respectively. The synthesis of N,O-CMC first forms -O-CH2COOH, then continues to form -NH-CH2COOH. This information is valuable to further optimize the reaction codition for CMC synthesis.

Rapid Construction of a Benzo-Fused Indoxamycin Core Enabled by Site-Selective C-H Functionalizations.

PubMed

Bedell, T Aaron; Hone, Graham A B; Valette, Damien; Yu, Jin-Quan; Davies, Huw M L; Sorensen, Erik J

2016-07-11

Methods for functionalizing carbon-hydrogen bonds are featured in a new synthesis of the tricyclic core architecture that characterizes the indoxamycin family of secondary metabolites. A unique collaboration between three laboratories has engendered a design for synthesis featuring two sequential C-H functionalization reactions, namely a diastereoselective dirhodium carbene insertion followed by an ester-directed oxidative Heck cyclization, to rapidly assemble the congested tricyclic core of the indoxamycins. This project exemplifies how multi-laboratory collaborations can foster conceptually novel approaches to challenging problems in chemical synthesis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

One period coupon bond valuation with revised first passage time approach and the application in Indonesian corporate bond

NASA Astrophysics Data System (ADS)

Maruddani, Di Asih I.; Rosadi, Dedi; Gunardic, Abdurakhman

2015-02-01

The value of a corporate bond is conventionally expressed in terms of zero coupon bond. In practice, the most common form of debt instrument is coupon bond and allows early default before maturity as safety covenant for the bondholder. This paper study valuation for one period coupon bond, a coupon bond that only give one time coupon at the bond period. It assumes that the model give bondholder the right to reorganize a firm if its value falls below a given barrier. Revised first passage time approach is applied for default time rule. As a result, formulas of equity, liability, and probability of default is derived for this specified model. Straightforward integration under risk neutral pricing is used for deriving those formulas. For the application, bond of Bank Rakyat Indonesia (BRI) as one of the largest bank in Indonesia is analyzed. R computing show that value of the equity is IDR 453.724.549.000.000, the liability is IDR 2.657.394.000.000, and the probability if default is 5.645305E-47 %.

A general mixture equation of state for double bonding carboxylic acids with ≥2 association sites

NASA Astrophysics Data System (ADS)

Marshall, Bennett D.

2018-05-01

In this paper, we obtain the first general multi-component solution to Wertheim's thermodynamic perturbation theory for the case that molecules can participate in cyclic double bonds. In contrast to previous authors, we do not restrict double bonding molecules to a 2-site association scheme. Each molecule in a multi-component mixture can have an arbitrary number of donor and acceptor association sites. The one restriction on the theory is that molecules can have at most one pair of double bonding sites. We also incorporate the effect of hydrogen bond cooperativity in cyclic double bonds. We then apply this new association theory to 2-site and 3-site models for carboxylic acids within the polar perturbed chain statistical associating fluid theory equation of state. We demonstrate the accuracy of the approach by comparison to both pure and multi-component phase equilibria data. It is demonstrated that the 3-site association model gives substantially a different hydrogen bonding structure than a 2-site approach. We also demonstrate that inclusion of hydrogen bond cooperativity has a substantial effect on a liquid phase hydrogen bonding structure.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Enantioselective functionalization of allylic C-H bonds following a strategy of functionalization and diversification.

PubMed

Sharma, Ankit; Hartwig, John F

2013-11-27

We report the enantioselective functionalization of allylic C-H bonds in terminal alkenes by a strategy involving the installation of a temporary functional group at the terminal carbon atom by C-H bond functionalization, followed by the catalytic diversification of this intermediate with a broad scope of reagents. The method consists of a one-pot sequence of palladium-catalyzed allylic C-H bond oxidation under neutral conditions to form linear allyl benzoates, followed by iridium-catalyzed allylic substitution. This overall transformation forms a variety of chiral products containing a new C-N, C-O, C-S, or C-C bond at the allylic position in good yield with a high branched-to-linear selectivity and excellent enantioselectivity (ee ≤97%). The broad scope of the overall process results from separating the oxidation and functionalization steps; by doing so, the scope of nucleophile encompasses those sensitive to direct oxidative functionalization. The high enantioselectivity of the overall process is achieved by developing an allylic oxidation that occurs without acid to form the linear isomer with high selectivity. These allylic functionalization processes are amenable to an iterative sequence leading to (1,n)-functionalized products with catalyst-controlled diastereo- and enantioselectivity. The utility of the method in the synthesis of biologically active molecules has been demonstrated.

Modeling the free-radical polymerization of hexanediol diacrylate (HDDA): a molecular dynamics and graph theory approach.

PubMed

Torres-Knoop, Ariana; Kryven, Ivan; Schamboeck, Verena; Iedema, Piet D

2018-05-02

In the printing, coating and ink industries, photocurable systems are becoming increasingly popular and multi-functional acrylates are one of the most commonly used monomers due to their high reactivity (fast curing). In this paper, we use molecular dynamics and graph theory tools to investigate the thermo-mechanical properties and topology of hexanediol diacrylate (HDDA) polymer networks. The gel point was determined as the point where a giant component was formed. For the conditions of our simulations, we found the gel point to be around 0.18 bond conversion. A detailed analysis of the network topology showed, unexpectedly, that the flexibility of the HDDA molecules plays an important role in increasing the conversion of double bonds, while delaying the gel point. This is due to a back-biting type of reaction mechanism that promotes the formation of small cycles. The glass transition temperature for several degrees of curing was obtained from the change in the thermal expansion coefficient. For a bond conversion close to experimental values we obtained a glass transition temperature around 400 K. For the same bond conversion we estimate a Young's modulus of 3 GPa. Both of these values are in good agreement with experiments.

System-size convergence of point defect properties: The case of the silicon vacancy

NASA Astrophysics Data System (ADS)

Corsetti, Fabiano; Mostofi, Arash A.

2011-07-01

We present a comprehensive study of the vacancy in bulk silicon in all its charge states from 2+ to 2-, using a supercell approach within plane-wave density-functional theory, and systematically quantify the various contributions to the well-known finite size errors associated with calculating formation energies and stable charge state transition levels of isolated defects with periodic boundary conditions. Furthermore, we find that transition levels converge faster with respect to supercell size when only the Γ-point is sampled in the Brillouin zone, as opposed to a dense k-point sampling. This arises from the fact that defect level at the Γ-point quickly converges to a fixed value which correctly describes the bonding at the defect center. Our calculated transition levels with 1000-atom supercells and Γ-point only sampling are in good agreement with available experimental results. We also demonstrate two simple and accurate approaches for calculating the valence band offsets that are required for computing formation energies of charged defects, one based on a potential averaging scheme and the other using maximally-localized Wannier functions (MLWFs). Finally, we show that MLWFs provide a clear description of the nature of the electronic bonding at the defect center that verifies the canonical Watkins model.

A CAD/CAM Zirconium Bar as a Bonded Mandibular Fixed Retainer: A Novel Approach with Two-Year Follow-Up.

PubMed

Zreaqat, Maen; Hassan, Rozita; Hanoun, Abdul Fatah

2017-01-01

Stainless steel alloys containing 8% to 12% nickel and 17% to 22% chromium are generally used in orthodontic appliances. A major concern has been the performance of alloys in the environment in which they are intended to function in the oral cavity. Biodegradation and metal release increase the risk of hypersensitivity and cytotoxicity. This case report describes for the first time a CAD/CAM zirconium bar as a bonded mandibular fixed retainer with 2-year follow-up in a patient who is subjected to long-term treatment with fixed orthodontic appliance and suspected to have metal hypersensitivity as shown by the considerable increase of nickel and chromium concentrations in a sample of patient's unstimulated saliva. The CAD/CAM design included a 1.8 mm thickness bar on the lingual surface of lower teeth from canine to canine with occlusal rests on mesial side of first premolars. For better retention, a thin layer of feldspathic ceramic was added to the inner surface of the bar and cemented with two dual-cured cement types. The patient's complaint subsided 6 weeks after cementation. Clinical evaluation appeared to give good functional value where the marginal fit of digitized CAD/CAM design and glazed surface offered an enhanced approach of fixed retention.

A CAD/CAM Zirconium Bar as a Bonded Mandibular Fixed Retainer: A Novel Approach with Two-Year Follow-Up

PubMed Central

Hassan, Rozita; Hanoun, Abdul Fatah

2017-01-01

Stainless steel alloys containing 8% to 12% nickel and 17% to 22% chromium are generally used in orthodontic appliances. A major concern has been the performance of alloys in the environment in which they are intended to function in the oral cavity. Biodegradation and metal release increase the risk of hypersensitivity and cytotoxicity. This case report describes for the first time a CAD/CAM zirconium bar as a bonded mandibular fixed retainer with 2-year follow-up in a patient who is subjected to long-term treatment with fixed orthodontic appliance and suspected to have metal hypersensitivity as shown by the considerable increase of nickel and chromium concentrations in a sample of patient's unstimulated saliva. The CAD/CAM design included a 1.8 mm thickness bar on the lingual surface of lower teeth from canine to canine with occlusal rests on mesial side of first premolars. For better retention, a thin layer of feldspathic ceramic was added to the inner surface of the bar and cemented with two dual-cured cement types. The patient's complaint subsided 6 weeks after cementation. Clinical evaluation appeared to give good functional value where the marginal fit of digitized CAD/CAM design and glazed surface offered an enhanced approach of fixed retention. PMID:28819572

Design and engineering of organic molecules for customizable Terahertz tags

NASA Astrophysics Data System (ADS)

Ray, Shaumik; Dash, Jyotirmayee; Nallappan, Kathirvel; Kaware, Vaibhav; Basutkar, Nitin; Ambade, Ashootosh; Joshi, Kavita; Pesala, Bala

2014-03-01

Terahertz (THz) frequency band lies between the microwave and infrared region of the electromagnetic spectrum. Molecules having strong resonances in this frequency range are ideal for realizing "Terahertz tags" which can be easily incorporated into various materials. THz spectroscopy of molecules, especially at frequencies below 10 THz, provides valuable information on the low frequency vibrational modes, viz. intermolecular vibrational modes, hydrogen bond stretching, torsional vibrations in several chemical and biological compounds. So far there have been very few attempts to engineer molecules which can demonstrate customizable resonances in the THz frequency region. In this paper, Diamidopyridine (DAP) based molecules are used as a model system to demonstrate engineering of THz resonances (< 10 THz) by fine-tuning the molecular mass and bond strengths. Density Functional Theory (DFT) simulations have been carried out to explain the origin of THz resonances and factors contributing to the shift in resonances due to the addition of various functional groups. The design approach presented here can be easily extended to engineer various organic molecules suitable for THz tags application.

Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins

DOE PAGES

Bondar, Ana-Nicoleta; Smith, Jeremy C.

2017-07-25

Channel and pump rhodopsins use energy from light absorbed by a covalently bound retinal chromophore to transport ions across membranes of microbial cells. Ion transfer steps, including proton transfer, can couple to changes in protein conformational dynamics and water positions. Although general principles of how microbial rhodopsins function are largely understood, key issues pertaining to reaction mechanisms remain unclear. Here, we compare the protonation-coupled dynamics of pump and channelrhodopsins, highlighting the roles that water dynamics, protein electrostatics and protein flexibility can have in ion transport mechanisms. We discuss observations supporting important functional roles of inter- and intra-helical carboxylate/hydroxyl hydrogen-bonding motifs.more » Specifically, we use the proton pump bacteriorhodopsin, the sodium pump KR2, channelrhodopsins and Anabaena sensory rhodopsin. We outline the usefulness of theoretic biophysics approaches to the study of retinal proteins, challenges in studying the hydrogen-bond dynamics of rhodopsin active sites, and implications for conformational coupling in membrane transporters.« less

Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins

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

Bondar, Ana-Nicoleta; Smith, Jeremy C.

Channel and pump rhodopsins use energy from light absorbed by a covalently bound retinal chromophore to transport ions across membranes of microbial cells. Ion transfer steps, including proton transfer, can couple to changes in protein conformational dynamics and water positions. Although general principles of how microbial rhodopsins function are largely understood, key issues pertaining to reaction mechanisms remain unclear. Here, we compare the protonation-coupled dynamics of pump and channelrhodopsins, highlighting the roles that water dynamics, protein electrostatics and protein flexibility can have in ion transport mechanisms. We discuss observations supporting important functional roles of inter- and intra-helical carboxylate/hydroxyl hydrogen-bonding motifs.more » Specifically, we use the proton pump bacteriorhodopsin, the sodium pump KR2, channelrhodopsins and Anabaena sensory rhodopsin. We outline the usefulness of theoretic biophysics approaches to the study of retinal proteins, challenges in studying the hydrogen-bond dynamics of rhodopsin active sites, and implications for conformational coupling in membrane transporters.« less

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.

[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.

Soluble expression of disulfide-bonded C-type lectin like domain of human CD93 in the cytoplasm of Escherichia coli.

PubMed

Nativel, Brice; Figuester, Audrey; Andries, Jessica; Planesse, Cynthia; Couprie, Joël; Gasque, Philippe; Viranaicken, Wildriss; Iwema, Thomas

2016-12-01

CD93 belongs to the group XIV C-type lectin like domain (CTLD) and is closely related to thrombomodulin (CD141). Although CD93 is known to be involved in the regulation of cell adhesion and phagocytosis, its role in innate immunity remains to be fully investigated. Critically, published data about CD141 suggest that CD93 CTLD could be involved in the control of inflammation. In order to address further functional and structural analyses, we expressed human CD93 CTLD with several disulfide bonds in an E. coli expression system. As the E. coli cytoplasm is a reducing compartment, production of disulfide-bond proteins remains a challenge. Hence, we decided to over express CD93 CTLD in commercially available strains of E. coli and co-expressed a sulfhydryl oxidase (Erv1p) and a disulfide isomerase (DsbC). This strategy led to high yield expression of a native form of CD93 CTLD. NMR studies revealed that Ca 2+ was not able to bind to CD93 CTLD. We also showed that the recombinant protein could alter LPS pro-inflammatory activity on THP1. This work provides new tool for further functional and structural studies to decipher the functions associated to the CTLD of CD93. This approach may also be used for others members of the group XIV C-type lectin like domain (CD141, CD248 and CLec14A). Copyright © 2016 Elsevier B.V. All rights reserved.

Covalent lanthanide(III) macrocyclic complexes: the bonding nature and optical properties of a promising single antenna molecule.

PubMed

Rabanal-León, Walter A; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

2014-12-21

The present work is focused on the elucidation of the electronic structure, bonding nature and optical properties of a series of low symmetry (C2) coordination compounds of type [Ln(III)HAM](3+), where "Ln(III)" are the trivalent lanthanide ions: La(3+), Ce(3+), Eu(3+) and Lu(3+), while "HAM" is the neutral six-nitrogen donor macrocyclic ligand [C22N6H26]. This systematic study has been performed in the framework of the Relativistic Density Functional Theory (R-DFT) and also using a multi-reference approach via the Complete Active Space (CAS) wavefunction treatment with the aim of analyzing their ground state and excited state electronic structures as well as electronic correlation. Furthermore, the use of the energy decomposition scheme proposed by Morokuma-Ziegler and the electron localization function (ELF) allows us to characterize the bonding between the lanthanide ions and the macrocyclic ligand, obtaining as a result a dative-covalent interaction. Due to a great deal of lanthanide optical properties and their technological applications, the absorption spectra of this set of coordination compounds were calculated using the time-dependent density functional theory (TD-DFT), where the presence of the intense Ligand to Metal Charge Transfer (LMCT) bands in the ultraviolet and visible region and the inherent f-f electronic transitions in the Near-Infra Red (NIR) region for some lanthanide ions allow us to propose these systems as "single antenna molecules" with potential applications in NIR technologies.

Generalized valence bond description of the ground states (X(1)Σg(+)) of homonuclear pnictogen diatomic molecules: N2, P2, and As2.

PubMed

Xu, Lu T; Dunning, Thom H

2015-06-09

The ground state, X1Σg+, of N2 is a textbook example of a molecule with a triple bond consisting of one σ and two π bonds. This assignment, which is usually rationalized using molecular orbital (MO) theory, implicitly assumes that the spins of the three pairs of electrons involved in the bonds are singlet-coupled (perfect pairing). However, for a six-electron singlet state, there are five distinct ways to couple the electron spins. The generalized valence bond (GVB) wave function lifts this restriction, including all of the five spin functions for the six electrons involved in the bond. For N2, we find that the perfect pairing spin function is indeed dominant at Re but that it becomes progressively less so from N2 to P2 and As2. Although the perfect pairing spin function is still the most important spin function in P2, the importance of a quasi-atomic spin function, which singlet couples the spins of the electrons in the σ orbitals while high spin coupling those of the electrons in the π orbitals on each center, has significantly increased relative to N2 and, in As2, the perfect pairing and quasi-atomic spin couplings are on essentially the same footing. This change in the spin coupling of the electrons in the bonding orbitals down the periodic table may contribute to the rather dramatic decrease in the strengths of the Pn2 bonds from N2 to As2 as well as in the increase in their chemical reactivity and should be taken into account in more detailed analyses of the bond energies in these species. We also compare the spin coupling in N2 with that in C2, where the quasi-atomic spin coupling dominants around Re.

A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids.

PubMed

Hou, Guangjin; Gupta, Rupal; Polenova, Tatyana; Vega, Alexander J

2014-02-01

Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1 H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN -symmetry based experiments, from which the principal components of the 1 H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1 H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U- 13 C, 15 N-labeled histdine demonstrating that 1 H chemical shift tensors can be reliably determined for the 1 H 15 N and 1 H 13 C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1 H(C) and 1 H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids.

Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis

PubMed Central

Park, In-Hee; Venable, John D.; Steckler, Caitlin; Cellitti, Susan E.; Lesley, Scott A.; Spraggon, Glen; Brock, Ansgar

2015-01-01

Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure and dynamics. More recently, Hydrogen Exchange Mass Spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from Molecular Dynamics (MD) simulation snapshots is used to determine partitioning over bonded and non-bonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for Fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of residue resolved protection factor predictions for staphylococcal nuclease with NMR data, which was also used to compare prediction performance with other algorithms described in the literature. The demonstrated transferable and scalable MD based HX prediction approach adds significantly to the available tools for HX-MS data interpretation based on available structures and models. PMID:26241692

Determination of apparent coupling factors for adhesive bonded acrylic plates using SEAL approach

NASA Astrophysics Data System (ADS)

Pankaj, Achuthan. C.; Shivaprasad, M. V.; Murigendrappa, S. M.

2018-04-01

Apparent coupling loss factors (CLF) and velocity responses has been computed for two lap joined adhesive bonded plates using finite element and experimental statistical energy analysis like approach. A finite element model of the plates has been created using ANSYS software. The statistical energy parameters have been computed using the velocity responses obtained from a harmonic forced excitation analysis. Experiments have been carried out for two different cases of adhesive bonded joints and the results have been compared with the apparent coupling factors and velocity responses obtained from finite element analysis. The results obtained from the studies signify the importance of modeling of adhesive bonded joints in computation of the apparent coupling factors and its further use in computation of energies and velocity responses using statistical energy analysis like approach.

Hydrogen Bonds and Life in the Universe.

PubMed

Vladilo, Giovanni; Hassanali, Ali

2018-01-03

The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a "covalent-bond stage" to a "hydrogen-bond stage" in prebiotic chemistry.

Hydrogen Bonds and Life in the Universe

PubMed Central

2018-01-01

The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a “covalent-bond stage” to a “hydrogen-bond stage” in prebiotic chemistry. PMID:29301382

Linear and nonlinear susceptibilities from diffusion quantum Monte Carlo: application to periodic hydrogen chains.

PubMed

Umari, P; Marzari, Nicola

2009-09-07

We calculate the linear and nonlinear susceptibilities of periodic longitudinal chains of hydrogen dimers with different bond-length alternations using a diffusion quantum Monte Carlo approach. These quantities are derived from the changes in electronic polarization as a function of applied finite electric field--an approach we recently introduced and made possible by the use of a Berry-phase, many-body electric-enthalpy functional. Calculated susceptibilities and hypersusceptibilities are found to be in excellent agreement with the best estimates available from quantum chemistry--usually extrapolations to the infinite-chain limit of calculations for chains of finite length. It is found that while exchange effects dominate the proper description of the susceptibilities, second hypersusceptibilities are greatly affected by electronic correlations. We also assess how different approximations to the nodal surface of the many-body wave function affect the accuracy of the calculated susceptibilities.

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.

Only Five of 10 Strictly Conserved Disulfide Bonds Are Essential for Folding and Eight for Function of the HIV-1 Envelope Glycoprotein

PubMed Central

van Anken, Eelco; Sanders, Rogier W.; Liscaljet, I. Marije; Land, Aafke; Bontjer, Ilja; Tillemans, Sonja; Nabatov, Alexey A.; Paxton, William A.; Berkhout, Ben

2008-01-01

Protein folding in the endoplasmic reticulum goes hand in hand with disulfide bond formation, and disulfide bonds are considered key structural elements for a protein's folding and function. We used the HIV-1 Envelope glycoprotein to examine in detail the importance of its 10 completely conserved disulfide bonds. We systematically mutated the cysteines in its ectodomain, assayed the mutants for oxidative folding, transport, and incorporation into the virus, and tested fitness of mutant viruses. We found that the protein was remarkably tolerant toward manipulation of its disulfide-bonded structure. Five of 10 disulfide bonds were dispensable for folding. Two of these were even expendable for viral replication in cell culture, indicating that the relevance of these disulfide bonds becomes manifest only during natural infection. Our findings refine old paradigms on the importance of disulfide bonds for proteins. PMID:18653472

Centrifuge Rotor Models: A Comparison of the Euler-Lagrange and the Bond Graph Modeling Approach

NASA Technical Reports Server (NTRS)

Granda, Jose J.; Ramakrishnan, Jayant; Nguyen, Louis H.

2006-01-01

A viewgraph presentation on centrifuge rotor models with a comparison using Euler-Lagrange and bond graph methods is shown. The topics include: 1) Objectives; 2) MOdeling Approach Comparisons; 3) Model Structures; and 4) Application.

Microplates with adaptive surfaces.

PubMed

Akbulut, Meshude; Lakshmi, Dhana; Whitcombe, Michael J; Piletska, Elena V; Chianella, Iva; Güven, Olgun; Piletsky, Sergey A

2011-11-14

Here we present a new and versatile method for the modification of the well surfaces of polystyrene microtiter plates (microplates) with poly(N-phenylethylene diamine methacrylamide), (poly-NPEDMA). The chemical grafting of poly-NPEDMA to the surface of microplates resulted in the formation of thin layers of a polyaniline derivative bearing pendant methacrylamide double bonds. These were used as the attachment point for various functional polymers through photochemical grafting of various, for example, acrylate and methacrylate, polymers with different functionalities. In a model experiment, we have modified poly-NPEDMA-coated microplates with a small library of polymers containing different functional groups using a two-step approach. In the first step, double bonds were activated by UV irradiation in the presence of N,N-diethyldithiocarbamic acid benzyl ester (iniferter). This enabled grafting of the polymer library in the second step by UV irradiation of solutions of the corresponding monomers in the microplate wells. The uniformity of coatings was confirmed spectrophotometrically, by microscopic imaging and by contact angle measurements (CA). The feasibility of the current technology has been shown by the generation of a small library of polymers grafted to the microplate well surfaces and screening of their affinity to small molecules, such as atrazine, a trio of organic dyes, and a model protein, bovine serum albumin (BSA). The stability of the polymers, reproducibility of measurement, ease of preparation, and cost-effectiveness make this approach suitable for applications in high-throughput screening in the area of materials research.

Test Cases for Modeling and Validation of Structures with Piezoelectric Actuators

NASA Technical Reports Server (NTRS)

Reaves, Mercedes C.; Horta, Lucas G.

2001-01-01

A set of benchmark test articles were developed to validate techniques for modeling structures containing piezoelectric actuators using commercially available finite element analysis packages. The paper presents the development, modeling, and testing of two structures: an aluminum plate with surface mounted patch actuators and a composite box beam with surface mounted actuators. Three approaches for modeling structures containing piezoelectric actuators using the commercially available packages: MSC/NASTRAN and ANSYS are presented. The approaches, applications, and limitations are discussed. Data for both test articles are compared in terms of frequency response functions from deflection and strain data to input voltage to the actuator. Frequency response function results using the three different analysis approaches provided comparable test/analysis results. It is shown that global versus local behavior of the analytical model and test article must be considered when comparing different approaches. Also, improper bonding of actuators greatly reduces the electrical to mechanical effectiveness of the actuators producing anti-resonance errors.

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.

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

The externally corrected coupled cluster approach with four- and five-body clusters from the CASSCF wave function.

PubMed

Xu, Enhua; Li, Shuhua

2015-03-07

An externally corrected CCSDt (coupled cluster with singles, doubles, and active triples) approach employing four- and five-body clusters from the complete active space self-consistent field (CASSCF) wave function (denoted as ecCCSDt-CASSCF) is presented. The quadruple and quintuple excitation amplitudes within the active space are extracted from the CASSCF wave function and then fed into the CCSDt-like equations, which can be solved in an iterative way as the standard CCSDt equations. With a size-extensive CASSCF reference function, the ecCCSDt-CASSCF method is size-extensive. When the CASSCF wave function is readily available, the computational cost of the ecCCSDt-CASSCF method scales as the popular CCSD method (if the number of active orbitals is small compared to the total number of orbitals). The ecCCSDt-CASSCF approach has been applied to investigate the potential energy surface for the simultaneous dissociation of two O-H bonds in H2O, the equilibrium distances and spectroscopic constants of 4 diatomic molecules (F2(+), O2(+), Be2, and NiC), and the reaction barriers for the automerization reaction of cyclobutadiene and the Cl + O3 → ClO + O2 reaction. In most cases, the ecCCSDt-CASSCF approach can provide better results than the CASPT2 (second order perturbation theory with a CASSCF reference function) and CCSDT methods.

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

Introducing new reactivity descriptors: "Bond reactivity indices." Comparison of the new definitions and atomic reactivity indices.

PubMed

Sánchez-Márquez, Jesús

2016-11-21

A new methodology to obtain reactivity indices has been defined. This is based on reactivity functions such as the Fukui function or the dual descriptor and makes it possible to project the information of reactivity functions over molecular orbitals instead of the atoms of the molecule (atomic reactivity indices). The methodology focuses on the molecule's natural bond orbitals (bond reactivity indices) because these orbitals (with physical meaning) have the advantage of being very localized, allowing the reaction site of an electrophile or nucleophile to be determined within a very precise molecular region. This methodology gives a reactivity index for every Natural Bond Orbital (NBO), and we have verified that they have equivalent information to the reactivity functions. A representative set of molecules has been used to test the new definitions. Also, the bond reactivity index has been related with the atomic reactivity one, and complementary information has been obtained from the comparison. Finally, a new atomic reactivity index has been defined and compared with previous definitions.

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.

Instant tough bonding of hydrogels for soft machines and electronics

PubMed Central

Wirthl, Daniela; Pichler, Robert; Drack, Michael; Kettlguber, Gerald; Moser, Richard; Gerstmayr, Robert; Hartmann, Florian; Bradt, Elke; Kaltseis, Rainer; Siket, Christian M.; Schausberger, Stefan E.; Hild, Sabine; Bauer, Siegfried; Kaltenbrunner, Martin

2017-01-01

Introducing methods for instant tough bonding between hydrogels and antagonistic materials—from soft to hard—allows us to demonstrate elastic yet tough biomimetic devices and machines with a high level of complexity. Tough hydrogels strongly attach, within seconds, to plastics, elastomers, leather, bone, and metals, reaching unprecedented interfacial toughness exceeding 2000 J/m2. Healing of severed ionic hydrogel conductors becomes feasible and restores function instantly. Soft, transparent multilayered hybrids of elastomers and ionic hydrogels endure biaxial strain with more than 2000% increase in area, facilitating soft transducers, generators, and adaptive lenses. We demonstrate soft electronic devices, from stretchable batteries, self-powered compliant circuits, and autonomous electronic skin for triggered drug delivery. Our approach is applicable in rapid prototyping and in delicate environments inaccessible for extended curing and cross-linking. PMID:28691092

Directing-Group-mediated C-H-Alkynylations.

PubMed

Caspers, Lucien D; Nachtsheim, Boris J

2018-05-18

C-C triple bonds are amongst the most versatile functional groups in synthetic chemistry. Complementary to the Sonogashira coupling the direct metal-catalyzed alkynylation of C-H bonds has emerged as a highly promising approach in recent years. To guarantee a high regioselectivity suitable directing groups (DGs) are necessary to guide the transition metal (TM) into the right place. In this Focus Review we present the current developments in DG-mediated C(sp 2 )-H and C(sp 3 )-H modifications with terminal alkynes under oxidative conditions and with electrophilic alkynylation reagents. We will discuss further modifications of the alkyne, in particular subsequent cyclizations to carbo- and heterocycles and modifications of the DG in the presence of the alkyne. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Instant tough bonding of hydrogels for soft machines and electronics.

PubMed

Wirthl, Daniela; Pichler, Robert; Drack, Michael; Kettlguber, Gerald; Moser, Richard; Gerstmayr, Robert; Hartmann, Florian; Bradt, Elke; Kaltseis, Rainer; Siket, Christian M; Schausberger, Stefan E; Hild, Sabine; Bauer, Siegfried; Kaltenbrunner, Martin

2017-06-01

Introducing methods for instant tough bonding between hydrogels and antagonistic materials-from soft to hard-allows us to demonstrate elastic yet tough biomimetic devices and machines with a high level of complexity. Tough hydrogels strongly attach, within seconds, to plastics, elastomers, leather, bone, and metals, reaching unprecedented interfacial toughness exceeding 2000 J/m 2 . Healing of severed ionic hydrogel conductors becomes feasible and restores function instantly. Soft, transparent multilayered hybrids of elastomers and ionic hydrogels endure biaxial strain with more than 2000% increase in area, facilitating soft transducers, generators, and adaptive lenses. We demonstrate soft electronic devices, from stretchable batteries, self-powered compliant circuits, and autonomous electronic skin for triggered drug delivery. Our approach is applicable in rapid prototyping and in delicate environments inaccessible for extended curing and cross-linking.

Density functional Gaussian-type-orbital approach to theoretical study of nitric oxide dimers

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

Jursic, B.S.; Zdravkovski, Z.

Structure and total energies of the cis NO dimer, the trans NO dimer, and the NO monomer were calculated by ab initio methods (UHF, UMP2, and MP3) and density functional theory methods (LSDA and BLYP) with different basis sets [from 3-21G* to 6-311++(3df,3pd)]. The system is especially hard to model because two NO molecules are weakly associated in a dimer that has very long N-N bond. The results obtained by different methods are compared and the necessity of correlational methods for studying these systems is discussed.

Multiple hydrogen bonding in excited states of aminopyrazine in methanol solution: time-dependent density functional theory study.

PubMed

Chai, Shuo; Yu, Jie; Han, Yong-Chang; Cong, Shu-Lin

2013-11-01

Aminopyrazine (AP) and AP-methanol complexes have been theoretically studied by using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The excited-state hydrogen bonds are discussed in detail. In the ground state the intermolecular multiple hydrogen bonds can be formed between AP molecule and protic solvents. The AP monomer and hydrogen-bonded complex of AP with one methanol are photoexcited initially to the S2 state, and then transferred to the S1 state via internal conversion. However the complex of AP with two methanol molecules is directly excited to the S1 state. From the calculated electronic excited energies and simulated absorption spectra, we find that the intermolecular hydrogen bonds are strengthened in the electronic excited states. The strengthening is confirmed by the optimized excited-state geometries. The photochemical processes in the electronic excited states are significantly influenced by the excited-state hydrogen bond strengthening. Copyright © 2013 Elsevier B.V. All rights reserved.

The direct arylation of allylic sp3 C–H bonds via organocatalysis and photoredox catalysis

PubMed Central

Cuthbertson, James D.; MacMillan, David W. C.

2015-01-01

The direct functionalization of unactivated sp3 C–H bonds is still one of the most challenging problems facing synthetic organic chemists. The appeal of such transformations derives from their capacity to facilitate the construction of complex organic molecules via the coupling of simple and otherwise inert building blocks, without introducing extraneous functional groups. Despite notable recent efforts,1 the establishment of general and mild strategies for the engagement of sp3 C–H bonds in carbon–carbon bond forming reactions has proven difficult. Within this context, the discovery of chemical transformations that are able to directly functionalize allylic methyl, methylene, and methine carbons in a catalytic manner is a priority. While protocols for direct allylic C–H oxidation and amination have become widely established,2,3 the engagement of allylic substrates in carbon–carbon bond-forming reactions has thus far required the use of pre-functionalized coupling partners.4 In particular, the direct arylation of non-functionalized allylic systems would enable chemists to rapidly access a series of known pharmacophores, though a general solution to this longstanding challenge remains elusive. We describe herein the use of both photoredox and organic catalysis to accomplish the first mild, broadly effective direct allylic C–H arylation. This new C–C bond-forming reaction readily accommodates a broad range of alkene and electron-deficient arene reactants and has been used in the direct arylation of benzylic C–H bonds. PMID:25739630

Rhodium(III)-Catalyzed Amidation of Unactivated C(sp(3) )-H Bonds.

PubMed

Wang, He; Tang, Guodong; Li, Xingwei

2015-10-26

Nitrogenation by direct functionalization of C-H bonds represents an important strategy for constructing C-N bonds. Rhodium(III)-catalyzed direct amidation of unactivated C(sp(3) )-H bonds is rare, especially under mild reaction conditions. Herein, a broad scope of C(sp(3) )-H bonds are amidated under rhodium catalysis in high efficiency using 3-substituted 1,4,2-dioxazol-5-ones as the amide source. The protocol broadens the scope of rhodium(III)-catalyzed C(sp(3) )-H activation chemistry, and is applicable to the late-stage functionalization of natural products. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rhodium(III)-catalyzed vinylic sp2 C-H bond functionalization: efficient synthesis of pyrido[1,2-α]benzimidazoles and imidazo[1,2-α]pyridines.

PubMed

Dong, Lin; Huang, Ji-Rong; Qu, Chuan-Hua; Zhang, Qian-Ru; Zhang, Wei; Han, Bo; Peng, Cheng

2013-09-28

A simple approach for synthesis of novel aza-fused scaffolds such as pyrido[1,2-α]benzimidazoles and imidazo[1,2-α]pyridines was developed by Rh(III)-catalyzed direct oxidative coupling between alkenes and unactivated alkynes without an extra directing group. The method would allow a broad substrate scope, providing fused heterocycles with potential biological properties.

Geminal difunctionalization of α-diazo arylmethylphosphonates: synthesis of fluorinated phosphonates.

PubMed

Zhou, Yujing; Zhang, Yan; Wang, Jianbo

2016-11-08

A general approach towards diverse fluorinated phosphonates via geminal difunctionalization reactions of α-diazo arylmethylphosphonates is described. The diazo functionality (RR'C[double bond, length as m-dash]N 2 ) is successfully converted to RR'CF 2 , RR'CHF, RR'CFBr or RR'CFNR'' 2 groups by employing different fluorination reagents. A variety of fluorinated organophosphorus compounds were readily accessed in good to excellent yields from a common type of precursor.

Communication: Density functional theory model for multi-reference systems based on the exact-exchange hole normalization

NASA Astrophysics Data System (ADS)

Laqua, Henryk; Kussmann, Jörg; Ochsenfeld, Christian

2018-03-01

The correct description of multi-reference electronic ground states within Kohn-Sham density functional theory (DFT) requires an ensemble-state representation, employing fractionally occupied orbitals. However, the use of fractional orbital occupation leads to non-normalized exact-exchange holes, resulting in large fractional-spin errors for conventional approximative density functionals. In this communication, we present a simple approach to directly include the exact-exchange-hole normalization into DFT. Compared to conventional functionals, our model strongly improves the description for multi-reference systems, while preserving the accuracy in the single-reference case. We analyze the performance of our proposed method at the example of spin-averaged atoms and spin-restricted bond dissociation energy surfaces.

Communication: Density functional theory model for multi-reference systems based on the exact-exchange hole normalization.

PubMed

Laqua, Henryk; Kussmann, Jörg; Ochsenfeld, Christian

2018-03-28

The correct description of multi-reference electronic ground states within Kohn-Sham density functional theory (DFT) requires an ensemble-state representation, employing fractionally occupied orbitals. However, the use of fractional orbital occupation leads to non-normalized exact-exchange holes, resulting in large fractional-spin errors for conventional approximative density functionals. In this communication, we present a simple approach to directly include the exact-exchange-hole normalization into DFT. Compared to conventional functionals, our model strongly improves the description for multi-reference systems, while preserving the accuracy in the single-reference case. We analyze the performance of our proposed method at the example of spin-averaged atoms and spin-restricted bond dissociation energy surfaces.

Subsystem density functional theory with meta-generalized gradient approximation exchange-correlation functionals.

PubMed

Śmiga, Szymon; Fabiano, Eduardo; Laricchia, Savio; Constantin, Lucian A; Della Sala, Fabio

2015-04-21

We analyze the methodology and the performance of subsystem density functional theory (DFT) with meta-generalized gradient approximation (meta-GGA) exchange-correlation functionals for non-bonded molecular systems. Meta-GGA functionals depend on the Kohn-Sham kinetic energy density (KED), which is not known as an explicit functional of the density. Therefore, they cannot be directly applied in subsystem DFT calculations. We propose a Laplacian-level approximation to the KED which overcomes this limitation and provides a simple and accurate way to apply meta-GGA exchange-correlation functionals in subsystem DFT calculations. The so obtained density and energy errors, with respect to the corresponding supermolecular calculations, are comparable with conventional approaches, depending almost exclusively on the approximations in the non-additive kinetic embedding term. An embedding energy error decomposition explains the accuracy of our method.

Application of the Covalent Bond Classification Method for the Teaching of Inorganic Chemistry

ERIC Educational Resources Information Center

Green, Malcolm L. H.; Parkin, Gerard

2014-01-01

The Covalent Bond Classification (CBC) method provides a means to classify covalent molecules according to the number and types of bonds that surround an atom of interest. This approach is based on an elementary molecular orbital analysis of the bonding involving the central atom (M), with the various interactions being classified according to the…

A continuum-based structural modeling approach for cellulose nanocrystals (CNCs)

Treesearch

Mehdi Shishehbor; Fernando L. Dri; Robert J. Moon; Pablo D. Zavattieri

2018-01-01

We present a continuum-based structural model to study the mechanical behavior of cel- lulose nanocrystals (CNCs), and analyze the effect of bonded and non-bonded interactions on the mechanical properties under various loading conditions. In particular, this model assumes the uncoupling between the bonded and non-bonded interactions and their be- havior is obtained...

Bond Dissociation Energies for Substituted Polycyclic Aromatic Hydrocarbons and Their Cations

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W.; Langhoff, Stephen R.; Arnold, James O. (Technical Monitor)

1998-01-01

The B3LYP/4-31G approach is used to compute bond energies for a series of substituted benzene, naphthalene, and anthracene molecules and their cations. The benzene bond energies are compared with experiment. The trends in the bond energies are discussed. The ionization energies are also reported and compared with available experiments.

Characterization of Long-Chain Fatty Acid as N-(4-Aminomethylphenyl) Pyridinium Derivative by MALDI LIFT-TOF/TOF Mass Spectrometry

NASA Astrophysics Data System (ADS)

Frankfater, Cheryl; Jiang, Xuntian; Hsu, Fong-Fu

2018-05-01

Charge remote fragmentation (CRF) elimination of CnH2n+2 residues along the aliphatic tail of long chain fatty acid is hall mark of keV high-energy CID fragmentation process. It is an important fragmentation pathway leading to structural characterization of biomolecules by CID tandem mass spectrometry. In this report, we describe MALDI LIFT TOF-TOF mass spectrometric approach to study a wide variety of fatty acids (FAs), which were derivatized to N-(4-aminomethylphenyl) pyridinium (AMPP) derivative, and desorbed as M+ ions by laser with or without matrix. The high-energy MALDI LIFT TOF-TOF mass spectra of FA-AMPP contain fragment ions mainly deriving from CRF cleavages of CnH2n+2 residues, as expected. These ions together with ions from specific cleavages of the bond(s) involving the functional group within the molecule provide more complete structural identification than those produced by low-energy CID/HCD using a linear ion-trap instrument. However, this LIFT TOF-TOF mass spectrometric approach inherits low sensitivity, a typical feature of high-energy CID tandem mass spectrometry. Because of the lack of unit mass precursor ion selection with sufficient sensitivity of the current LIFT TOF-TOF technology, product ion spectra from same chain length fatty acids with difference in one or two double bonds in a mixture are not distinguishable.

Hydrogen bonding in malonaldehyde: a density functional and reparametrized semiempirical approach

NASA Astrophysics Data System (ADS)

Kovačević, Goran; Hrenar, Tomica; Došlić, Nadja

2003-08-01

Intramolecular proton transfer in malonaldehyde (MA) has been investigated by density functional theory (DFT). The DFT results were used for the construction of a high quality semiempirical potential energy surface with a reparametrized PM3 Hamiltonian. A two-step reparameterization procedure is proposed in which (i) the PM3-MAIS core-core functions for the O-H and H-H interactions were used and a new functional form for the O-O correction function was proposed and (ii) a set of specific reaction parameters (SRP) has been obtained via genetic algorithm optimization. The quality of the reparametrized semiempirical potential energy surfaces was tested by calculating the tunneling splitting of vibrational levels and the anharmonic vibrational frequencies of the system. The applicability to multi-dimensional dynamics in large molecular systems is discussed.

Extending density functional embedding theory for covalently bonded systems.

PubMed

Yu, Kuang; Carter, Emily A

2017-12-19

Quantum embedding theory aims to provide an efficient solution to obtain accurate electronic energies for systems too large for full-scale, high-level quantum calculations. It adopts a hierarchical approach that divides the total system into a small embedded region and a larger environment, using different levels of theory to describe each part. Previously, we developed a density-based quantum embedding theory called density functional embedding theory (DFET), which achieved considerable success in metals and semiconductors. In this work, we extend DFET into a density-matrix-based nonlocal form, enabling DFET to study the stronger quantum couplings between covalently bonded subsystems. We name this theory density-matrix functional embedding theory (DMFET), and we demonstrate its performance in several test examples that resemble various real applications in both chemistry and biochemistry. DMFET gives excellent results in all cases tested thus far, including predicting isomerization energies, proton transfer energies, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps for local chromophores. Here, we show that DMFET systematically improves the quality of the results compared with the widely used state-of-the-art methods, such as the simple capped cluster model or the widely used ONIOM method.

Facile synthesis of -C[double bond, length as m-dash]N- linked covalent organic frameworks under ambient conditions.

PubMed

Ding, San-Yuan; Cui, Xiao-Hui; Feng, Jie; Lu, Gongxuan; Wang, Wei

2017-10-31

We reported herein a facile approach for the synthesis of -C[double bond, length as m-dash]N- linked covalent organic frameworks under ambient conditions. Three known (COF-42, COF-43, and COF-LZU1) and one new (Pr-COF-42) COF materials were successfully synthesized using this method. Furthermore, this simple synthetic approach makes the large-scale synthesis of -C[double bond, length as m-dash]N- linked COFs feasible.

Correlated hydrogen bonding fluctuations and vibrational cross peaks in N-methyl acetamide: simulation based on a complete electrostatic density functional theory map.

PubMed

Hayashi, Tomoyuki; Mukamel, Shaul

2006-11-21

The coherent nonlinear response of the entire amide line shapes of N-methyl acetamide to three infrared pulses is simulated using an electrostatic density functional theory map. Positive and negative cross peaks contain signatures of correlations between the fundamentals and the combination state. The amide I-A and I-III cross-peak line shapes indicate positive correlation and anticorrelation of frequency fluctuations, respectively. These can be ascribed to correlated hydrogen bonding at C[double bond]O and N-H sites. The amide I frequency is negatively correlated with the hydrogen bond on carbonyl C[double bond]O, whereas the amide A and III are negatively and positively correlated, respectively, with the hydrogen bond on amide N-H.

Efficient Organometallic Spin Filter between Single-Wall Carbon Nanotube or Graphene Electrodes

NASA Astrophysics Data System (ADS)

Koleini, Mohammad; Paulsson, Magnus; Brandbyge, Mads

2007-05-01

We present a theoretical study of spin transport in a class of molecular systems consisting of an organometallic benzene-vanadium cluster placed in between graphene or single-wall carbon-nanotube-model contacts. Ab initio modeling is performed by combining spin density functional theory and nonequilibrium Green’s function techniques. We consider weak and strong cluster-contact bonds. Depending on the bonding we find from 73% (strong bonds) up to 99% (weak bonds) spin polarization of the electron transmission, and enhanced polarization with increased cluster length.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta.

PubMed

Combs, Steven A; Mueller, Benjamin K; Meiler, Jens

2018-05-29

Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identify and evaluate these PCIs through analyzing the geometry between participating atoms. However, we hypothesize that PCIs can be unified through a simplified electron orbital representation. To test this hypothesis, we have introduced orbital based chemical descriptors for PCIs into Rosetta, called the PCI score function. Optimal geometries for the PCIs are derived from a statistical analysis of high-quality protein structures obtained from the Protein Data Bank (PDB), and the relative orientation of electron deficient hydrogen atoms and electron-rich lone pair or π orbitals are evaluated. We demonstrate that nativelike geometries of hydrogen bonds, salt bridges, cation-π, and π-π interactions are recapitulated during minimization of protein conformation. The packing density of tested protein structures increased from the standard score function from 0.62 to 0.64, closer to the native value of 0.70. Overall, rotamer recovery improved when using the PCI score function (75%) as compared to the standard Rosetta score function (74%). The PCI score function represents an improvement over the standard Rosetta score function for protein model scoring; in addition, it provides a platform for future directions in the analysis of small molecule to protein interactions, which depend on partial covalent interactions.

Construction of Well-Defined Redox-Responsive CO2 -Based Polycarbonates: Combination of Immortal Copolymerization and Prereaction Approach.

PubMed

Liu, Shunjie; Zhao, Xun; Guo, Hongchen; Qin, Yusheng; Wang, Xianhong; Wang, Fosong

2017-05-01

Due to the axial group initiation in traditional (salen)CoX/quaternary ammonium catalyst system, it is difficult to construct single active center propagating polycarbonates for copolymerization of CO 2 /epoxides. Here a redox-responsive poly(vinyl cyclohexene carbonate) (PVCHC) with detachable disulfide-bond backbone is synthesized in a controllable manner using (salen)CoTFA/[bis(triphenylphosphine)iminium, [PPN]TFA binary catalyst, where the axial group initiation is depressed by judiciously choosing 3,3'-dithiodipropionic acid as starter. While for those comonomers failing to obtain polycarbonate with unimodal gel permeation chromatography (GPC) curve, a versatile method is developed by combination of immortal copolymerization and prereaction approach, and functional aliphatic polycarbonates having well-defined architecture and narrow polydispersity can be prepared. The resulting PVCHC can be further functionalized with alkenes by versatile cross-metathesis reaction to tune the physicochemical properties. The combination of immortal polymerization and prereaction approach creates a powerful platform for controllable synthesis of functional CO 2 -based polycarbonates. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-pressure phase diagram of hydrogen and deuterium sulfides from first principles: Structural and vibrational properties including quantum and anharmonic effects

NASA Astrophysics Data System (ADS)

Bianco, Raffaello; Errea, Ion; Calandra, Matteo; Mauri, Francesco

2018-06-01

We study the structural and vibrational properties of the high-temperature superconducting sulfur trihydride and trideuteride in the high-pressure I m 3 ¯m and R 3 m phases by first-principles density-functional-theory calculations. On lowering pressure, the rhombohedral transition I m 3 ¯m →R 3 m is expected, with hydrogen-bond desymmetrization and occurrence of trigonal lattice distortion. With both Perdew-Burke-Ernzerhof (PBE) and Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional, in hydrostatic conditions we find that, contrary to what is suggested in some recent experiments, if the rhombohedral distortion exists it affects mainly the hydrogen bonds, whereas the resulting cell distortion is minimal. We estimate that the occurrence of a stress anisotropy of approximately 10 % could explain this discrepancy. Assuming hydrostatic conditions, we calculate the critical pressure at which the rhombohedral transition occurs. Quantum and anharmonic effects, which are relevant in this system, are included at nonperturbative level with the stochastic self-consistent harmonic approximation. Within this approach, we determine the transition pressure by calculating the free-energy Hessian, a method that allows to estimate the critical pressure with much higher precision (and much lower computational cost) compared with the free-energy "finite-difference" approach previously used. Using PBE and BLYP, we find that quantum anharmonic effects are responsible for a strong reduction of the critical pressure with respect to the one obtained with the classical harmonic approach. Interestingly, for the two functionals, even if the transition pressures at classical harmonic level differ by 83 GPa, the transition pressures including quantum anharmonic effects differ only by 23 GPa. Moreover, we observe a prominent isotope effect, as we estimate higher transition pressure for D3S than for H3S . Finally, within the stochastic self-consistent harmonic approximation, with PBE we calculate the anharmonic phonon spectral functions in the I m 3 ¯m phase. The strong anharmonicity of the system is confirmed by the occurrence of very large anharmonic broadenings leading to complex non-Lorentzian line shapes. Generally, for the high-energy hydrogen bond-stretching modes, the anharmonic phonon broadening is of the same magnitude of the electron-phonon one. However, for the vibrational spectra at zone center, accessible, e.g., by infrared spectroscopy, the broadenings are very small (linewidth at most around 2 meV) and anharmonic phonon quasiparticles are well defined.

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

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.

Spectroscopic analysis and charge transfer interaction studies of 4-benzyloxy-2-nitroaniline insecticide: A density functional theoretical approach

NASA Astrophysics Data System (ADS)

Arul Dhas, D.; Hubert Joe, I.; Roy, S. D. D.; Balachandran, S.

2015-01-01

A widespread exploration on the intra-molecular charge transfer interaction through an efficient π-conjugated path from a strong electron-donor group (amino) to a strong electron-acceptor group (nitro) has been carried out using FTIR, FT-Raman, UV-Vis, fluorescence and NMR spectra on insecticide compound 4-benzyloxy-2-nitroaniline. Density functional theory method is used to determine optimized molecular geometry, harmonic vibrational wavenumbers and intensities using 6-311G(d,p) basis set by means of Gaussian 09W program suit. A comprehensive investigation on the sp2 to sp3 hybridization and non-planarity property has been performed. Natural bond orbital analysis is used to study the existence of C-H⋯O, N-H⋯O and C-H⋯π proper and improper hydrogen bonds. The HOMO and LUMO analysis reveals the possibility of charge transfer within the molecule. A complete assignment of the experimental absorption peaks in the ultraviolet region has also been performed. Isotropic chemical shifts of 13C, 1H, 15N and 18O NMR and nuclear spin-spin coupling constants have been computed using the gauge-invariant atomic orbital method. The biological activity of substituent amino and nitro groups are evident from the hydrogen bonds through which the target amino acids are linked to the drug as evidenced from molecular docking.

The Self-Association of Graphane Is Driven by London Dispersion and Enhanced Orbital Interactions.

PubMed

Wang, Changwei; Mo, Yirong; Wagner, J Philipp; Schreiner, Peter R; Jemmis, Eluvathingal D; Danovich, David; Shaik, Sason

2015-04-14

We investigated the nature of the cohesive energy between graphane sheets via multiple CH···HC interactions, using density functional theory (DFT) including dispersion correction (Grimme's D3 approach) computations of [n]graphane σ dimers (n = 6-73). For comparison, we also evaluated the binding between graphene sheets that display prototypical π/π interactions. The results were analyzed using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory. BLW interprets the intermolecular interactions in terms of frozen interaction energy (ΔE(F)) composed of electrostatic and Pauli repulsion interactions, polarization (ΔE(pol)), charge-transfer interaction (ΔE(CT)), and dispersion effects (ΔE(disp)). The BLW analysis reveals that the cohesive energy between graphane sheets is dominated by two stabilizing effects, namely intermolecular London dispersion and two-way charge transfer energy due to the σ(CH) → σ*(HC) interactions. The shift of the electron density around the nonpolar covalent C-H bonds involved in the intermolecular interaction decreases the C-H bond lengths uniformly by 0.001 Å. The ΔE(CT) term, which accounts for ∼15% of the total binding energy, results in the accumulation of electron density in the interface area between two layers. This accumulated electron density thus acts as an electronic "glue" for the graphane layers and constitutes an important driving force in the self-association and stability of graphane under ambient conditions. Similarly, the "double faced adhesive tape" style of charge transfer interactions was also observed among graphene sheets in which it accounts for ∼18% of the total binding energy. The binding energy between graphane sheets is additive and can be expressed as a sum of CH···HC interactions, or as a function of the number of C-H bonds.

Two-State Reactivity in Low-Valent Iron-Mediated C-H Activation and the Implications for Other First-Row Transition Metals.

PubMed

Sun, Yihua; Tang, Hao; Chen, Kejuan; Hu, Lianrui; Yao, Jiannian; Shaik, Sason; Chen, Hui

2016-03-23

C-H bond activation/functionalization promoted by low-valent iron complexes has recently emerged as a promising approach for the utilization of earth-abundant first-row transition metals to carry out this difficult transformation. Herein we use extensive density functional theory and high-level ab initio coupled cluster calculations to shed light on the mechanism of these intriguing reactions. Our key mechanistic discovery for C-H arylation reactions reveals a two-state reactivity (TSR) scenario in which the low-spin Fe(II) singlet state, which is initially an excited state, crosses over the high-spin ground state and promotes C-H bond cleavage. Subsequently, aryl transmetalation occurs, followed by oxidation of Fe(II) to Fe(III) in a single-electron transfer (SET) step in which dichloroalkane serves as an oxidant, thus promoting the final C-C coupling and finalizing the C-H functionalization. Regeneration of the Fe(II) catalyst for the next round of C-H activation involves SET oxidation of the Fe(I) species generated after the C-C bond coupling. The ligand sphere of iron is found to play a crucial role in the TSR mechanism by stabilization of the reactive low-spin state that mediates the C-H activation. This is the first time that the successful TSR concept conceived for high-valent iron chemistry is shown to successfully rationalize the reactivity for a reaction promoted by low-valent iron complexes. A comparative study involving other divalent middle and late first-row transition metals implicates iron as the optimum metal in this TSR mechanism for C-H activation. It is predicted that stabilization of low-spin Mn(II) using an appropriate ligand sphere should produce another promising candidate for efficient C-H bond activation. This new TSR scenario therefore emerges as a new strategy for using low-valent first-row transition metals for C-H activation reactions.

Can Geographic Bridging Social Capital Improve the Health of People Who Live in Deprived Urban Neighborhoods?

PubMed

Kim, Chang-O; Cho, Byong-Hee

2016-10-01

The growing number of people living in deprived urban neighborhoods, which often have unhealthy environments, is of growing concern to inequality researchers. Social capital could be a resource to help such communities get ahead. In this study, we examined the differential effects of bonding and bridging social capital on self-rated health using two operational definitions, which we call personal and geographic social capital. Bonding and bridging social capital were operationally distinguished as respondents' perceived similarity to other members of a group with respect to personal characteristics (personal social capital) or as structural similarity with respect to geographical location (geographic social capital). The results showed that although both bonding and bridging social capital as defined by person-based criteria were associated with increased odds of self-rated health compared to those who reported zero participation, when defined by place-based criteria, only bridging social capital was associated with increased odds of self-rated health; no clear association was found between health and belonging to groups within the neighborhood, so-called geographic bonding social capital. The present study suggests that geographic bridging social capital can function as linking social capital that enables an upward approach depending on the political and economic contexts of urbanization. © The Author(s) 2015.

Divergent palladium iodide catalyzed multicomponent carbonylative approaches to functionalized isoindolinone and isobenzofuranimine derivatives.

PubMed

Mancuso, Raffaella; Ziccarelli, Ida; Armentano, Donatella; Marino, Nadia; Giofrè, Salvatore V; Gabriele, Bartolo

2014-04-18

2-Alkynylbenzamides underwent different reaction pathways when allowed to react under PdI2-catalyzed oxidative carbonylation conditions, depending on the nature of the external nucleophile and reaction conditions. Thus, oxidative carbonylation of 2-ethynylbenzamides, bearing a terminal triple bond, carried out in the presence of a secondary amine as external nucleophile, selectively led to the formation of 3-[(dialkylcarbamoyl)methylene]isoindolin-1-ones through the intermediate formation of the corresponding 2-ynamide derivatives followed by intramolecular nucleophilic attack by the nitrogen of the benzamide moiety on the conjugated triple bond. On the other hand, 3-[(alkoxycarbonyl)methylene]isobenzofuran-1(3H)imines were selectively obtained when the oxidative carbonylation of 2-alkynylbenzamides, bearing a terminal or an internal triple bond, was carried out in the presence of an alcohol R'OH (such as methanol or ethanol) as the external nucleophile and HC(OR')3 as a dehydrating agent, necessary to avoid substrate hydrolysis. In this latter case, the reaction pathway leading to the isobenzofuranimine corresponded to the 5-exo-dig intramolecular nucleophilic attack of the oxygen of the benzamide moiety on the triple bond coordinated to the metal center followed by alkoxycarbonylation. The structures of representative products have been confirmed by X-ray crystallographic analysis.

Free energy landscape of protein-like chains with discontinuous potentials

NASA Astrophysics Data System (ADS)

Movahed, Hanif Bayat; van Zon, Ramses; Schofield, Jeremy

2012-06-01

In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond interactions, electrostatic repulsion, and covalent bond vibrations are modeled by discontinuous step, shoulder, and square-well potentials, respectively. The protein-like chains exhibit a secondary alpha helix structure in their folded states at low temperatures, and allow a natural definition of a configuration by considering which beads are bonded. Free energies and entropies of configurations are computed using the parallel tempering method in combination with hybrid Monte Carlo sampling of the canonical ensemble of the discontinuous potential system. The probability of observing the most common configuration is used to analyze the nature of the free energy landscape, and it is found that the model with the least number of possible bonds exhibits a funnel-like free energy landscape at low enough temperature for chains with fewer than 30 beads. For longer proteins, the free landscape consists of several minima, where the configuration with the lowest free energy changes significantly by lowering the temperature and the probability of observing the most common configuration never approaches one due to the degeneracy of the lowest accessible potential energy.

Comparison of micro push-out bond strengths of two fiber posts luted using simplified adhesive approaches.

PubMed

Mumcu, Emre; Erdemir, Ugur; Topcu, Fulya Toksoy

2010-05-01

By means of a micro push-out test, this study compared the bond strengths of two types of fiber-reinforced posts cemented with luting cements based on two currently available adhesive approaches as well as evaluated their failure modes. Sixty extracted single-rooted human maxillary central incisor and canine teeth were sectioned below the cementoenamel junction, and the roots were endodontically treated. Following standardized post space preparation, the roots were divided into two fiber post groups and then further into three subgroups of 10 specimens each according to the luting cements. A push-out test was performed to measure regional bond strengths, and the fracture modes were evaluated using a stereomicroscope. At the root section, there were no statistically significant differences (p>0.05) in push-out bond strength among the tested luting cements. Nevertheless, the push-out bond strength values of glass fiber-reinforced posts were higher than those of carbon fiber-reinforced posts, irrespective of the adhesive approach used. On failure mode, the predominant failure mode was adhesive failure between dentin and the luting cement.

Indium Zinc Oxide Mediated Wafer Bonding for III-V/Si Tandem Solar Cells

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

Tamboli, Adele C.; Essig, Stephanie; Horowitz, Kelsey A. W.

Silicon-based tandem solar cells are desirable as a high efficiency, economically viable approach to one sun or low concentration photovoltaics. We present an approach to wafer bonded III-V/Si solar cells using amorphous indium zinc oxide (IZO) as an interlayer. We investigate the impact of a heavily doped III-V contact layer on the electrical and optical properties of bonded test samples, including the predicted impact on tandem cell performance. We present economic modeling which indicates that the path to commercial viability for bonded cells includes developing low-cost III-V growth and reducing constraints on material smoothness. If these challenges can be surmounted,more » bonded tandems on Si can be cost-competitive with incumbent PV technologies, especially in low concentration, single axis tracking systems.« less

A density functional theory for colloids with two multiple bonding associating sites.

PubMed

Haghmoradi, Amin; Wang, Le; Chapman, Walter G

2016-06-22

Wertheim's multi-density formalism is extended for patchy colloidal fluids with two multiple bonding patches. The theory is developed as a density functional theory to predict the properties of an associating inhomogeneous fluid. The equation of state developed for this fluid depends on the size of the patch, and includes formation of cyclic, branched and linear clusters of associated species. The theory predicts the density profile and the fractions of colloids in different bonding states versus the distance from one wall as a function of bulk density and temperature. The predictions from our theory are compared with previous results for a confined fluid with four single bonding association sites. Also, comparison between the present theory and Monte Carlo simulation indicates a good agreement.

Experimental and Theoretical Approaches for the Surface Interaction between Copper and Activated Sludge Microorganisms at Molecular Scale

NASA Astrophysics Data System (ADS)

Luo, Hong-Wei; Chen, Jie-Jie; Sheng, Guo-Ping; Su, Ji-Hu; Wei, Shi-Qiang; Yu, Han-Qing

2014-11-01

Interactions between metals and activated sludge microorganisms substantially affect the speciation, immobilization, transport, and bioavailability of trace heavy metals in biological wastewater treatment plants. In this study, the interaction of Cu(II), a typical heavy metal, onto activated sludge microorganisms was studied in-depth using a multi-technique approach. The complexing structure of Cu(II) on microbial surface was revealed by X-ray absorption fine structure (XAFS) and electron paramagnetic resonance (EPR) analysis. EPR spectra indicated that Cu(II) was held in inner-sphere surface complexes of octahedral coordination with tetragonal distortion of axial elongation. XAFS analysis further suggested that the surface complexation between Cu(II) and microbial cells was the distorted inner-sphere coordinated octahedra containing four short equatorial bonds and two elongated axial bonds. To further validate the results obtained from the XAFS and EPR analysis, density functional theory calculations were carried out to explore the structural geometry of the Cu complexes. These results are useful to better understand the speciation, immobilization, transport, and bioavailability of metals in biological wastewater treatment plants.

A quantum informational approach for dissecting chemical reactions

NASA Astrophysics Data System (ADS)

Duperrouzel, Corinne; Tecmer, Paweł; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

2015-02-01

We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and π-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

Chemical intuition for high thermoelectric performance in monolayer black phosphorus, α-arsenene and aW-antimonene

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

Peng, Bo; Zhang, Hao; Shao, Hezhu

Identifying materials with intrinsically high thermoelectric performance remains a challenge even with the aid of a high-throughput search. Here, using a chemically intuitive approach based on the bond-orbital theory, three anisotropic 2D group-V materials (monolayer black phosphorus, α-arsenene, and aW-antimonene) are identified as candidates for high thermoelectric energy conversion efficiency. Concepts, such as bond length, bond angle, and bond strength, are used to explain the trends in their electronic properties, such as the band gap and the effective mass. Our first principles calculations confirm that high carrier mobilities and large Seebeck coefficients can be obtained at the same time inmore » these materials, due to complex Fermi surfaces originating from the anisotropic structures. An intuitive understanding of how the bonding character affects phonon transport is also provided with emphasis on the importance of bonding strength and bond anharmonicity. High thermoelectric performance is observed in these materials. In conclusion, our approach provides a powerful tool to identify new thermoelectric materials and evaluate their transport properties.« less

Chemical intuition for high thermoelectric performance in monolayer black phosphorus, α-arsenene and aW-antimonene

DOE PAGES

Peng, Bo; Zhang, Hao; Shao, Hezhu; ...

2017-11-21

Identifying materials with intrinsically high thermoelectric performance remains a challenge even with the aid of a high-throughput search. Here, using a chemically intuitive approach based on the bond-orbital theory, three anisotropic 2D group-V materials (monolayer black phosphorus, α-arsenene, and aW-antimonene) are identified as candidates for high thermoelectric energy conversion efficiency. Concepts, such as bond length, bond angle, and bond strength, are used to explain the trends in their electronic properties, such as the band gap and the effective mass. Our first principles calculations confirm that high carrier mobilities and large Seebeck coefficients can be obtained at the same time inmore » these materials, due to complex Fermi surfaces originating from the anisotropic structures. An intuitive understanding of how the bonding character affects phonon transport is also provided with emphasis on the importance of bonding strength and bond anharmonicity. High thermoelectric performance is observed in these materials. In conclusion, our approach provides a powerful tool to identify new thermoelectric materials and evaluate their transport properties.« less

Social play among juvenile wild Japanese macaques (Macaca fuscata) strengthens their social bonds.

PubMed

Shimada, Masaki; Sueur, Cédric

2018-01-01

Social play and grooming are typical affiliative interactions for many primate species, and are thought to have similar biological functions. However, grooming increases with age, whereas social play decreases. We proposed the hypothesis that both social grooming and social play in juveniles strengthen their social bonds in daily activities. We carried out field research on the social relationships among juvenile wild Japanese macaques in a troop in Kinkazan, Miyagi Prefecture, Japan, from fall 2007 to spring 2008 to investigate this hypothesis. We evaluated three relationships among juveniles, play indices (PI), grooming indices (GI), and 3-m-proximity indices (3mI) of each dyad (i.e., interacting pair), and compared these social networks based on the matrices of the indices. The play and grooming networks were correlated with the association network throughout the two research periods. The multiple network level measurements of the play network, but not the grooming network, resembled those of the association network. Using a causal step approach, we showed that social play and grooming interactions in fall seem to predict associations in the following spring, controlling for the PI and GI matrix in spring, respectively. Social play and grooming for each juvenile were negatively correlated. The results partially support our predictions; therefore, the hypothesis that the biological function of social play among immature Japanese macaques is to strengthen their social bonds in the near future and develop their social life appears to be correct. For juvenile macaques, social play, rather than grooming, functions as an important social mechanism to strengthen affiliative relationships. © 2017 Wiley Periodicals, Inc.

Ignition probability of polymer-bonded explosives accounting for multiple sources of material stochasticity

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

Kim, S.; Barua, A.; Zhou, M., E-mail: min.zhou@me.gatech.edu

2014-05-07

Accounting for the combined effect of multiple sources of stochasticity in material attributes, we develop an approach that computationally predicts the probability of ignition of polymer-bonded explosives (PBXs) under impact loading. The probabilistic nature of the specific ignition processes is assumed to arise from two sources of stochasticity. The first source involves random variations in material microstructural morphology; the second source involves random fluctuations in grain-binder interfacial bonding strength. The effect of the first source of stochasticity is analyzed with multiple sets of statistically similar microstructures and constant interfacial bonding strength. Subsequently, each of the microstructures in the multiple setsmore » is assigned multiple instantiations of randomly varying grain-binder interfacial strengths to analyze the effect of the second source of stochasticity. Critical hotspot size-temperature states reaching the threshold for ignition are calculated through finite element simulations that explicitly account for microstructure and bulk and interfacial dissipation to quantify the time to criticality (t{sub c}) of individual samples, allowing the probability distribution of the time to criticality that results from each source of stochastic variation for a material to be analyzed. Two probability superposition models are considered to combine the effects of the multiple sources of stochasticity. The first is a parallel and series combination model, and the second is a nested probability function model. Results show that the nested Weibull distribution provides an accurate description of the combined ignition probability. The approach developed here represents a general framework for analyzing the stochasticity in the material behavior that arises out of multiple types of uncertainty associated with the structure, design, synthesis and processing of materials.« less

Bonding thermoplastic polymers

DOEpatents

Wallow, Thomas I [Fremont, CA; Hunter, Marion C [Livermore, CA; Krafcik, Karen Lee [Livermore, CA; Morales, Alfredo M [Livermore, CA; Simmons, Blake A [San Francisco, CA; Domeier, Linda A [Danville, CA

2008-06-24

We demonstrate a new method for joining patterned thermoplastic parts into layered structures. The method takes advantage of case-II permeant diffusion to generate dimensionally controlled, activated bonding layers at the surfaces being joined. It is capable of producing bonds characterized by cohesive failure while preserving the fidelity of patterned features in the bonding surfaces. This approach is uniquely suited to production of microfluidic multilayer structures, as it allows the bond-forming interface between plastic parts to be precisely manipulated at micrometer length scales. The bond enhancing procedure is easily integrated in standard process flows and requires no specialized equipment.

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.

The role of higher-order terms in perturbation approaches to the monomer and\\xA0bonding contributions in a SAFT-type equation of state for square-well chain\\xA0fluids

NASA Astrophysics Data System (ADS)

Solana, J. R.; Akhouri, B. P.

2018-07-01

A perturbation theory for square-well chain fluids is developed within the scheme of the (generalised) Wertheim thermodynamic perturbation theory. The theory is based on the Pavlyukhin parametrisations [Y. T. Pavlyukhin, J. Struct. Chem. 53, 476 (2012)] of their simulation data for the first four perturbation terms in the high temperature expansion of the Helmholtz free energy of square-well monomer fluids combined with a second-order perturbation theory for the contact value of the radial distribution function of the square-well monomer fluid that enters into bonding contribution. To obtain the latter perturbation terms, we have performed computer simulations in the hard-sphere reference system. The importance of the perturbation terms beyond the second-order one for the monomer fluid and of the approximations of different orders in the bonding contribution for the chain fluids in the predicted equation of state, excess energy and liquid-vapour coexistence densities is analysed.

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.

Tunable anomalous hall effect induced by interfacial catalyst in perpendicular multilayers

NASA Astrophysics Data System (ADS)

Zhang, J. Y.; Peng, W. L.; Sun, Q. Y.; Liu, Y. W.; Dong, B. W.; Zheng, X. Q.; Yu, G. H.; Wang, C.; Zhao, Y. C.; Wang, S. G.

2018-04-01

The interfacial structures, playing a critical role on the transport properties and the perpendicular magnetic anisotropy in thin films and multilayers, can be modified by inserting an ultrathin functional layer at the various interfaces. The anomalous Hall effect (AHE) in the multilayers with core structure of Ta/CoFeB/X/MgO/Ta (X: Hf or Pt) is tuned by interfacial catalytic engineering. The saturation anomalous Hall resistance (RAH) is increased by 16.5% with 0.1 nm Hf insertion compared with the reference sample without insertion. However, the RAH value is decreased by 9.0% with 0.1 nm Pt insertion. The interfacial states were characterized by the X-ray photoelectron spectroscopy (XPS). The XPS results indicate that a strong bonding between Hf and O for Hf insertion, but no bonding between Pt and O for Pt insertion. The bonding between metal and oxygen leads to various oxygen migration behavior at the interfaces. Therefore, the opposite behavior about the RAH originates from the different oxygen behavior due to various interfacial insertion. This work provides a new approach to manipulate spin transport property for the potential applications.

Critical role in CXCR4 signaling and internalization of the polypeptide main chain in the amino terminus of SDF-1α probed by novel N-methylated synthetically and modularly modified chemokine analogues.

PubMed

Dong, Chang-Zhi; Tian, Shaomin; Choi, Won-Tak; Kumar, Santhosh; Liu, Dongxiang; Xu, Yan; Han, Xiaofeng; Huang, Ziwei; An, Jing

2012-07-31

The replication of human immunodeficiency virus type 1 (HIV-1) can be profoundly inhibited by the natural ligands of two major HIV-1 coreceptors, CXCR4 and CCR5. Stromal cell-derived factor-1α (SDF-1α) is a natural ligand of CXCR4. We have recently developed a synthetic biology approach of using synthetically and modularly modified (SMM)-chemokines to dissect various aspects of the structure-function relationship of chemokines and their receptors. Here, we used this approach to design novel SMM-SDF-1α analogues containing unnatural N-methylated residues in the amino terminus to investigate whether the polypeptide main chain amide bonds in the N-terminus of SDF-1α play a role in SDF-1α signaling via CXCR4 and/or receptor internalization. The results show that SDF-1α analogues with a modified N-methylated main chain at position 2, 3, or 5 retain significant CXCR4 binding and yet completely lose signaling activities. Furthermore, a representative N-methylated analogue has been shown to be incapable of causing CXCR4 internalization. These results suggest that the ability of SDF-1α to activate CXCR4 signaling and internalization is dependent upon the main chain amide bonds in the N-terminus of SDF-1α. This study demonstrates the feasibility and value of applying a synthetic biology approach to chemically engineer natural proteins and peptide ligands as probes of important biological functions that are not addressed by other biological techniques.

Opioid system and human emotions.

PubMed

Nummenmaa, Lauri; Tuominen, Lauri

2017-04-10

Emotions are states of vigilant readiness that guide human and animal behaviour during survival-salient situations. Categorical models of emotions posit neurally and physiologically distinct basic human emotions (anger, fear, disgust, happiness, sadness and surprise) that govern different survival functions. Opioid receptors are expressed abundantly in the mammalian emotion circuit, and the opioid system modulates a variety of functions related to arousal and motivation. Yet, its specific contribution to different basic emotions has remained poorly understood. Here, we review how the endogenous opioid system and particularly the μ receptor contribute to emotional processing in humans. Activation of the endogenous opioid system is consistently associated with both pleasant and unpleasant emotions. In general, exogenous opioid agonists facilitate approach-oriented emotions (anger, pleasure) and inhibit avoidance-oriented emotions (fear, sadness). Opioids also modulate social bonding and affiliative behaviour, and prolonged opioid abuse may render both social bonding and emotion recognition circuits dysfunctional. However, there is no clear evidence that the opioid system is able to affect the emotions associated with surprise and disgust. Taken together, the opioid systems contribute to a wide array of positive and negative emotions through their general ability to modulate the approach versus avoidance motivation associated with specific emotions. Because of the protective effects of opioid system-mediated prosociality and positive mood, the opioid system may constitute an important factor contributing to psychological and psychosomatic resilience. © 2017 The British Pharmacological Society.

Family Functioning and Parental Bonding During Childhood in Adults Diagnosed With ADHD.

PubMed

Montejo, José E; Durán, Mariona; Del Mar Martínez, María; Hilari, Ainoa; Roncalli, Nicoletta; Vilaregut, Anna; Corrales, Montserrat; Nogueira, Mariana; Casas, Miguel; Linares, Juan Luis; Ramos-Quiroga, J Antoni

2015-08-24

This work assesses family functioning, parental bonding, and the relationship between the two in adults diagnosed with ADHD. The study used a retrospective, ex post facto design and consisted of 100 adult participants, who were distributed into two groups: with and without diagnosis of ADHD. Two family assessment instruments were applied: the Family Adaptability and Cohesion Evaluation Scale short spanish version (FACES-20esp)) and the Parental Bonding Instrument (PBI). The diagnosis of ADHD was done by using a semistructured interview for Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV) criteria (Conners' Adult ADHD Diagnostic Interview for DSM-IV [CAADID]). The results showed that higher rigidity and lower emotional connection were significantly associated with ADHD family functioning. Regarding parental bonding, the results showed significant differences only in the care dimension, with the ADHD group reporting lower care than the control group. The results suggest that ADHD families present dysfunctional family functioning with a rigid, separated typology, and parental bonding based on control without affection. © 2015 SAGE Publications.

A computational study on choline benzoate and choline salicylate ionic liquids in the pure state and after CO2 adsorption.

PubMed

Aparicio, Santiago; Atilhan, Mert

2012-08-02

Choline-based ionic liquids show very adequate environmental, toxicological, and economical profiles for their application in many different technological areas. We report in this work a computational study on the properties of choline benzoate and choline salicylate ionic liquids, as representatives of this family of compounds, in the pure state and after CO(2) adsorption. Quantum chemistry calculations using the density functional theory approach for ionic pairs and ions, CO(2) pairs, were carried out, and the results analyzed using natural bond orbital and atoms in a molecule approaches. Classical molecular dynamics simulations of ionic liquids were done as a function of pressure, temperature, and CO(2) concentration. Microscopic structuring and intermolecular forces are analyzed together with the dynamic behavior of the studied fluids.

Fabrication and Characterization of Diffusion Bonds for Silicon Carbide

NASA Technical Reports Server (NTRS)

Halbig, Michael; Singh, Mrityunjay; Martin, Richard E.; Cosgriff, Laura M.

2007-01-01

Diffusion bonds of silicon carbide (SiC) were fabricated using several different types of titanium (Ti) based interlayers between the SiC substrates. The interlayers were an alloyed Ti foil, a pure Ti foil, and a physically vapor deposited (PVD) Ti coating. Microscopy was conducted to evaluate the cross-sections of the resulting bonds. Microprobe analysis identified reaction formed phases in the diffusion bonded region. Uniform and well adhered bonds were formed between the SiC substrates. In the case where the alloyed Ti foil or a thick Ti coating (i.e. 20 micron) was used as the interlayer, microcracks and several phases were present in the diffusion bonds. When a thinner interlayer was used (i.e. 10 micron PVD Ti), no microcracks were observed and only two reaction formed phases were present. The two phases were preferred and fully reacted phases that did not introduce thermal stresses or microcracks during the cool-down stage after processing. Diffusion bonded samples were evaluated with the non-destructive evaluation (NDE) methods of pulsed thermography and immersion ultrasonic testing. Joined SiC substrates that were fully bonded and that had simulated bond flaws in the interlayer were also evaluated using immersion ultrasound. Pull testing was conducted on the bonds to determine the tensile strength. To demonstrate the joining approach for a complex multilayered component for a low NOx injector application, the diffusion bonding approach was used to join three 4" diameter SiC discs that contained complex fuel and air flow channels.

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.

Automatic determination of fault effects on aircraft functionality

NASA Technical Reports Server (NTRS)

Feyock, Stefan

1989-01-01

The problem of determining the behavior of physical systems subsequent to the occurrence of malfunctions is discussed. It is established that while it was reasonable to assume that the most important fault behavior modes of primitive components and simple subsystems could be known and predicted, interactions within composite systems reached levels of complexity that precluded the use of traditional rule-based expert system techniques. Reasoning from first principles, i.e., on the basis of causal models of the physical system, was required. The first question that arises is, of course, how the causal information required for such reasoning should be represented. The bond graphs presented here occupy a position intermediate between qualitative and quantitative models, allowing the automatic derivation of Kuipers-like qualitative constraint models as well as state equations. Their most salient feature, however, is that entities corresponding to components and interactions in the physical system are explicitly represented in the bond graph model, thus permitting systematic model updates to reflect malfunctions. Researchers show how this is done, as well as presenting a number of techniques for obtaining qualitative information from the state equations derivable from bond graph models. One insight is the fact that one of the most important advantages of the bond graph ontology is the highly systematic approach to model construction it imposes on the modeler, who is forced to classify the relevant physical entities into a small number of categories, and to look for two highly specific types of interactions among them. The systematic nature of bond graph model construction facilitates the process to the point where the guidelines are sufficiently specific to be followed by modelers who are not domain experts. As a result, models of a given system constructed by different modelers will have extensive similarities. Researchers conclude by pointing out that the ease of updating bond graph models to reflect malfunctions is a manifestation of the systematic nature of bond graph construction, and the regularity of the relationship between bond graph models and physical reality.

13C and 19F solid-state NMR and X-ray crystallographic study of halogen-bonded frameworks featuring nitrogen-containing heterocycles.

PubMed

Szell, Patrick M J; Gabriel, Shaina A; Gill, Russell D D; Wan, Shirley Y H; Gabidullin, Bulat; Bryce, David L

2017-03-01

Halogen bonding is a noncovalent interaction between the electrophilic region of a halogen (σ-hole) and an electron donor. We report a crystallographic and structural analysis of halogen-bonded compounds by applying a combined X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) approach. Single-crystal XRD was first used to characterize the halogen-bonded cocrystals formed between two fluorinated halogen-bond donors (1,4-diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene) and several nitrogen-containing heterocycles (acridine, 1,10-phenanthroline, 2,3,5,6-tetramethylpyrazine, and hexamethylenetetramine). New structures are reported for the following three cocrystals, all in the P2 1 /c space group: acridine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 13 H 9 N, 1,10-phenanthroline-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 12 H 8 N 2 , and 2,3,5,6-tetramethylpyrazine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C 6 F 3 I 3 ·C 8 H 12 N 2 . 13 C and 19 F solid-state magic-angle spinning (MAS) NMR is shown to be a convenient method to characterize the structural features of the halogen-bond donor and acceptor, with chemical shifts attributable to cocrystal formation observed in the spectra of both nuclides. Cross polarization (CP) from 19 F to 13 C results in improved spectral sensitivity in characterizing the perfluorinated halogen-bond donor when compared to conventional 1 H CP. Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of magnetic shielding constants, along with optimization of the XRD structures, provide a final set of structures in best agreement with the experimental 13 C and 19 F chemical shifts. Data for carbons bonded to iodine remain outliers due to well-known relativistic effects.

Ionic bonding of lanthanides, as influenced by d- and f-atomic orbitals, by core-shells and by relativity.

PubMed

Ji, Wen-Xin; Xu, Wei; Schwarz, W H Eugen; Wang, Shu-Guang

2015-03-15

Lanthanide trihalide molecules LnX3 (X = F, Cl, Br, I) were quantum chemically investigated, in particular detail for Ln = Lu (lutetium). We applied density functional theory (DFT) at the nonrelativistic and scalar and SO-coupled relativistic levels, and also the ab initio coupled cluster approach. The chemically active electron shells of the lanthanide atoms comprise the 5d and 6s (and 6p) valence atomic orbitals (AO) and also the filled inner 4f semivalence and outer 5p semicore shells. Four different frozen-core approximations for Lu were compared: the (1s(2) -4d(10) ) [Pd] medium core, the [Pd+5s(2) 5p(6) = Xe] and [Pd+4f(14) ] large cores, and the [Pd+4f(14) +5s(2) 5p(6) ] very large core. The errors of LuX bonding are more serious on freezing the 5p(6) shell than the 4f(14) shell, more serious upon core-freezing than on the effective-core-potential approximation. The LnX distances correlate linearly with the AO radii of the ionic outer shells, Ln(3+) -5p(6) and X(-) -np(6) , characteristic for dominantly ionic Ln(3+) -X(-) binding. The heavier halogen atoms also bind covalently with the Ln-5d shell. Scalar relativistic effects contract and destabilize the LuX bonds, spin orbit coupling hardly affects the geometries but the bond energies, owing to SO effects in the free atoms. The relativistic changes of bond energy BE, bond length Re , bond force k, and bond stretching frequency vs do not follow the simple rules of Badger and Gordy (Re ∼BE∼k∼vs ). The so-called degeneracy-driven covalence, meaning strong mixing of accidentally near-degenerate, nearly nonoverlapping AOs without BE contribution is critically discussed. © 2015 Wiley Periodicals, Inc.

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

Xiong, Qi-lin, E-mail: xiongql@hust.edu.cn; Hubei Key Laboratory of Engineering Structural Analysis and Safety Assessment, Luoyu Road 1037, Wuhan 430074; Tian, Xiao Geng

The torsional mechanical properties of hexagonal single-walled boron nitride nanotubes (SWBNNTs), single-walled carbon nanotubes (SWCNTs), and their hybrid structures (SWBN-CNTs) are investigated using molecular dynamics (MD) simulation. Two approaches - force approach and energy approach, are adopted to calculate the shear moduli of SWBNNTs and SWCNTs, the discrepancy between two approaches is analyzed. The results show that the shear moduli of single-walled nanotubes (SWNTs), including SWBNNTs and SWCNTs are dependent on the diameter, especially for armchair SWNTs. The armchair SWNTs show the better ability of resistance the twisting comparable to the zigzag SWNTs. The effects of diameter and length onmore » the critical values of torque of SWNTs are obtained by comparing the torsional behaviors of SWNTs with different diameters and different lengths. It is observed that the MD results of the effect of diameter and length on the critical values of torque agrees well with the prediction of continuum shell model. The shear modulus of SWBN-CNT has a significant dependence on the percentages of SWCNT and the hybrid style has also an influence on shear modulus. The critical values of torque of SWBN-CNTs increase with the increase of the percentages of SWCNT. This phenomenon can be interpreted by the function relationship between the torque of different bonds (B-N-X, C-C-X, C-B-X, C-N-X) and the angles of bonds.« less

Supramolecular Recognition Allows Remote, Site-Selective C-H Oxidation of Methylenic Sites in Linear Amines.

PubMed

Olivo, Giorgio; Farinelli, Giulio; Barbieri, Alessia; Lanzalunga, Osvaldo; Di Stefano, Stefano; Costas, Miquel

2017-12-18

Site-selective C-H functionalization of aliphatic alkyl chains is a longstanding challenge in oxidation catalysis, given the comparable relative reactivity of the different methylenes. A supramolecular, bioinspired approach is described to address this challenge. A Mn complex able to catalyze C(sp 3 )-H hydroxylation with H 2 O 2 is equipped with 18-benzocrown-6 ether receptors that bind ammonium substrates via hydrogen bonding. Reversible pre-association of protonated primary aliphatic amines with the crown ether selectively exposes remote positions (C8 and C9) to the oxidizing unit, resulting in a site-selective oxidation. Remarkably, such control of selectivity retains its efficiency for a whole series of linear amines, overriding the intrinsic reactivity of C-H bonds, no matter the chain length. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dielectric and diamagnetic susceptibilities near percolative superconductor-insulator transitions.

PubMed

Loh, Yen Lee; Karki, Pragalv

2017-10-25

Coarse-grained superconductor-insulator composites exhibit a superconductor-insulator transition governed by classical percolation, which should be describable by networks of inductors and capacitors. We study several classes of random inductor-capacitor networks on square lattices. We present a unifying framework for defining electric and magnetic response functions, and we extend the Frank-Lobb bond-propagation algorithm to compute these quantities by network reduction. We confirm that the superfluid stiffness scales approximately as [Formula: see text] as the superconducting bond fraction p approaches the percolation threshold p c . We find that the diamagnetic susceptibility scales as [Formula: see text] below percolation, and as [Formula: see text] above percolation. For models lacking self-capacitances, the electric susceptibility scales as [Formula: see text]. Including a self-capacitance on each node changes the critical behavior to approximately [Formula: see text].

The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations.

PubMed

Lefebvre, Corentin; Khartabil, Hassan; Boisson, Jean-Charles; Contreras-García, Julia; Piquemal, Jean-Philip; Hénon, Eric

2018-03-19

Extraction of the chemical interaction signature from local descriptors based on electron density (ED) is still a fruitful field of development in chemical interpretation. In a previous work that used promolecular ED (frozen ED), the new descriptor, δg , was defined. It represents the difference between a virtual upper limit of the ED gradient (∇ρIGM , IGM=independent gradient model) that represents a noninteracting system and the true ED gradient (∇ρ ). It can be seen as a measure of electron sharing brought by ED contragradience. A compelling feature of this model is to provide an automatic workflow that extracts the signature of interactions between selected groups of atoms. As with the noncovalent interaction (NCI) approach, it provides chemists with a visual understanding of the interactions present in chemical systems. ∇ρIGM is achieved simply by using absolute values upon summing the individual gradient contributions that make up the total ED gradient. Hereby, we extend this model to relaxed ED calculated from a wave function. To this end, we formulated gradient-based partitioning (GBP) to assess the contribution of each orbital to the total ED gradient. We highlight these new possibilities across two prototypical examples of organic chemistry: the unconventional hexamethylbenzene dication, with a hexa-coordinated carbon atom, and β-thioaminoacrolein. It will be shown how a bond-by-bond picture can be obtained from a wave function, which opens the way to monitor specific interactions along reaction paths. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modified low-temperture direct bonding method for vacuum microelectronics application

NASA Astrophysics Data System (ADS)

Ju, Byeong-Kwon; Lee, Duck-Jung; Choi, Woo-Beom; Lee, Yun-Hi; Jang, Jin; Lee, Kwang-Bae; Oh, Myung-Hwan

1997-06-01

This paper presents the process and experimental results for the improved silicon-to-glass bonding using silicon direct bonding (SDB) followed by anodic bonding. The initial bonding between glass and silicon was caused by the hydrophilic surfaces of silicon-glass ensemble using SDB method. Then the initially bonded specimen had to be strongly bonded by anodic bonding process. The effects of the bonding process parameters on the interface energy were investigated as functions of the bonding temperature and voltage. We found that the specimen which was bonded using SDB process followed by anodic bonding process had higher interface energy than one using anodic bonding process only. The main factor contributing to the higher interface energy in the glass-to-silicon assemble bonded by SDB followed by anodic bonding was investigated by secondary ion mass spectroscopy analysis.

Effect of in vitro chewing and bruxism events on remineralization, at the resin-dentin interface.

PubMed

Toledano, Manuel; Cabello, Inmaculada; Aguilera, Fátima S; Osorio, Estrella; Osorio, Raquel

2015-01-02

The purpose of this study was to evaluate if different in vitro functional and parafunctional habits promote mineralization at the resin-dentin interface after bonding with three different adhesive approaches. Dentin surfaces were subjected to distinct treatments: demineralization by (1) 37% phosphoric acid (PA) followed by application of an etch-and-rinse dentin adhesive, Single Bond (SB) (PA+SB); (2) 0.5 M ethylenediaminetetraacetic acid (EDTA) followed by SB (EDTA+SB); (3) application of a self-etch dentin adhesive, Clearfil SE Bond (SEB). Different loading waveforms were applied: No cycling (I), cycled in sine (II) or square (III) waves, sustained loading hold for 24 h (IV) or sustained loading hold for 72 h (V). Remineralization at the bonded interfaces was assessed by AFM imaging/nano-indentation, Raman spectroscopy and Masson's trichrome staining. In general, in vitro chewing and parafunctional habits, promoted an increase of nano-mechanical properties at the resin-dentin interface. Raman spectroscopy through cluster analysis demonstrated an augmentation of the mineral-matrix ratio in loaded specimens. Trichrome staining reflected a narrow demineralized dentin matrix after loading in all groups except in PA+SB and EDTA+SB samples after sustained loading hold for 72 h, which exhibited a strong degree of mineralization. In vitro mechanical loading, produced during chewing and bruxism (square or hold 24 and 72 h waveforms), induced remineralization at the resin-dentin bonded interface. Copyright © 2014 Elsevier Ltd. All rights reserved.

Novel poly(dimethylsiloxane) bonding strategy via room temperature "chemical gluing".

PubMed

Lee, Nae Yoon; Chung, Bong Hyun

2009-04-09

Here we propose a new scheme for bonding poly(dimethylsiloxane) (PDMS), namely, a "chemical gluing", at room temperature by anchoring chemical functionalities on the surfaces of PDMS. Aminosilane and epoxysilane are anchored separately on the surfaces of two PDMS substrates, the reaction of which are well-known to form a strong amine-epoxy bond, therefore acting as a chemical glue. The bonding is performed for 1 h at room temperature without employing heat. We characterize the surface properties and composition by contact angle measurement, X-ray photoelectron spectroscopy analysis, and fluorescence measurement to confirm the formation of surface functionalities and investigate the adhesion strength by means of pulling, tearing, and leakage tests. As confirmed by the above-mentioned analyses and tests, PDMS surfaces were successfully modified with amine and epoxy functionalities, and a bonding based on the amine-epoxy chemical gluing was successfully realized within 1 h at room temperature. The bonding was sufficiently robust to tolerate intense introduction of liquid whose per minute injection volume was almost 2000 times larger than the total internal volume of the microchannel used. In addition to the bonding of PDMS-PDMS homogeneous assembly, the bonding of the PDMS-poly(ethylene terephthalate) heterogeneous assembly was also examined. We also investigate the potential use of the multifunctionalized walls inside the microchannel, generated as a consequence of the chemical gluing, as a platform for the targeted immobilization.

DNA-linked NanoParticle Lattices with Diamond Symmetry: Stability, Shape and Optical Properties

NASA Astrophysics Data System (ADS)

Emamy, Hamed; Tkachenko, Alexei; Gang, Oleg; Starr, Francis

The linking of nanoparticles (NP) by DNA has been proven to be an effective means to create NP lattices with specific order. Lattices with diamond symmetry are predicted to offer novel photonic properties, but self-assembly of such lattices has proven to be challenging due to the low packing fraction, sensitivity to bond orientation, and local heterogeneity. Recently, we reported an approach to create diamond NP lattices based on the association between anisotropic particles with well-defined tetravalent DNA binding topology and isotropically functionalized NP. Here, we use molecular dynamics simulations to evaluate the Gibbs free energy of these lattices, and thereby determine the stability of these lattices as a function of NP size and DNA stiffness. We also predict the equilibrium shape for the cubic diamond crystallite using the Wulff construction method. Specifically, we predict the equilibrium shape using the surface energy for different crystallographic planes. We evaluate surface energy directly form molecular dynamics simulation, which we correlate with theoretical estimates from the expected number of broken DNA bonds along a facet. Furthermore we study the optical properties of this structure, e.g optical bandgap.

A density functional theory study on the interactions between dibenzothiophene and tetrafluoroborate-based ionic liquids.

PubMed

Lin, Jin; Lü, Renqing; Wu, Chongchong; Xiao, Ye; Liang, Fei; Famakinwa, Temilola

2017-04-01

The interactions between dibenzothiophene (DBT) and N-butyl-N-methylimidazolium tetrafluoroborate ([BMIM][BF 4 ]), N-butyl-N-methylmorpholinium tetrafluoroborate ([Bmmorpholinium][BF 4 ]), N-butyl-N-methylpiperdinium tetrafluoroborate ([BMPiper][BF 4 ]), N-butyl-N-methylpyrrolidinium tetrafluoroborate ([BMPyrro][BF 4 ]), and N-butylpyridinium tetrafluoroborate ([BPY][BF 4 ]) were investigated using density functional theory approach. Geometric, electron, and topological properties were analyzed using natural bond orbital, atoms in molecules theory, and noncovalent interaction methods in order to understand intermolecular interactions between DBT and ionic liquids. The result shows that hydrogen bond and van der Waals interactions are widespread in all the ionic liquids-DBT systems. Ion-π interactions between DBT and cation or anion are also observed, while π + -π interactions are only found in the [BMIM][BF 4 ]-DBT and [BPY][BF 4 ]-DBT systems. The order of interaction energy is [BPY][BF4]-DBT > [BMIM][BF 4 ]-DBT > [BMPiper][BF 4 ]-DBT > [BMPyrro][BF 4 ]-DBT > [BMmorpholinum][BF 4 ]-DBT. The energies between DBT and the two ionic liquids containing aromatic cations are significantly higher.

Reaction mechanisms and kinetics of the elimination processes of 2-chloroethylsilane and derivatives: A DFT study using CTST, RRKM, and BET theories

NASA Astrophysics Data System (ADS)

Shiroudi, Abolfazl; Zahedi, Ehsan; Oliaey, Ahmad Reza; Deleuze, Michael S.

2017-03-01

The thermal decomposition kinetics of 2-chloroethylsilane and derivatives in the gas phase has been studied computationally using density functional theory, along with various exchange-correlation functionals (UM06-2x and ωB97XD) and the aug-cc-pVTZ basis set. The calculated energy profile has been supplemented with calculations of kinetic rate constants under atmospheric pressure and in the fall-off regime, using transition state theory (TST) and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Activation energies and rate constants obtained using the UM06-2x/aug-cc-pVTZ approach are in good agreement with the experimental data. The decomposition of 2-chloroethyltriethylsilane species into the related products [C2H4 + Et3SiCl] is characterized by 6 successive structural stability domains associated to the sequence of catastrophes C8H19SiCl: 6-C†FCC†[FF]-0: C6H15SiCl + C2H4. Breaking of Si-C bonds and formation of Si-Cl bonds occur in the vicinity of the transition state.

Spectroscopic characterization of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea and assessment of reactive and optoelectronic properties employing DFT calculations and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

War, Javeed Ahmad; Jalaja, K.; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Srivastava, Santosh Kumar; Van Alsenoy, C.

2017-02-01

IR and Raman spectra of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea (HIPPT) have been recorded in the solid phase and the vibrational wave numbers are calculated theoretically by B3LYP/6-31G(d,p) (6D, 7F) method. All the fundamental vibrational modes have been assigned using potential energy distribution values and the molecular structure was analyzed in terms of parameters like bond length, bond angles and dihedral angles. The ring breathing mode of the phenyl ring is observed at 1016 cm-1 in the IR spectrum, 1014 cm-1 in the Raman spectrum and at 1014 cm-1 theoretically. The values of polarizability and hyperpolarizabilities were calculated and nonlinear optical properties are discussed. The HOMO-LUMO plot reveals the charge transfer possibilities in the molecule. The NBO analysis was computed and possible transitions were correlated with the electronic transitions. In the title compound, the imidazole ring and CH2 groups are tilted from each other and the thiourea group is tilted from the phenyl ring. Using MEP plot the electrophilic and nucleophilic regions are identified. Local reactivity properties were investigated by analysis of ALIE surfaces and Fukui functions. Oxidation and degradation properties were initially assessed by calculation of bond dissociation energies of all single acyclic bonds. Determination of atoms with pronounced interactions with water molecules was performed by calculation of radial distribution functions after molecular dynamics simulations. Chargehopping rates were calculated within Marcus semi-empiric approach, employing both DFT calculations and MD simulations. The molecular docking computational predictions were complemented by the in vitro antibacterial activity evaluation.

Quantum treatment of protons with the reduced explicitly correlated Hartree-Fock approach

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

Sirjoosingh, Andrew; Pak, Michael V.; Brorsen, Kurt R.

2015-06-07

The nuclear-electronic orbital (NEO) approach treats select nuclei quantum mechanically on the same level as the electrons and includes nonadiabatic effects between the electrons and the quantum nuclei. The practical implementation of this approach is challenging due to the significance of electron-nucleus dynamical correlation. Herein, we present a general extension of the previously developed reduced NEO explicitly correlated Hartree-Fock (RXCHF) approach, in which only select electronic orbitals are explicitly correlated to each quantum nuclear orbital via Gaussian-type geminal functions. Approximations of the electronic exchange between the geminal-coupled electronic orbitals and the other electronic orbitals are also explored. This general approachmore » enables computationally tractable yet accurate calculations on molecular systems with quantum protons. The RXCHF method is applied to the hydrogen cyanide (HCN) and FHF{sup −} systems, where the proton and all electrons are treated quantum mechanically. For the HCN system, only the two electronic orbitals associated with the CH covalent bond are geminal-coupled to the proton orbital. For the FHF{sup −} system, only the four electronic orbitals associated with the two FH covalent bonds are geminal-coupled to the proton orbital. For both systems, the RXCHF method produces qualitatively accurate nuclear densities, in contrast to mean field-based NEO approaches. The development and implementation of the RXCHF method provide the framework to perform calculations on systems such as proton-coupled electron transfer reactions, where electron-proton nonadiabatic effects are important.« less

Site specific interaction between ZnO nanoparticles and tyrosine: A density functional theory study

NASA Astrophysics Data System (ADS)

Singh, Satvinder; Singh, Janpreet; Singh, Baljinder; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

2018-05-01

First Principles Calculations have been performed on ZnO/Tyrosine atomic complex to study site specific interaction of Tyrosine and ZnO nanoparticles. Calculated results shows that -COOH group present in Tyrosine is energetically more favorable than -NH2 group. Interactions show ionic bonding between ZnO and Tyrosine. All the calculations have been performed under the Density Functional Theory (DFT) framework. Structural and electronic properties of (ZnO)3/Tyrosine complex have been studied. Gaussian basis set approach has been adopted for the calculations. A ring type most stable (ZnO)3 atomic cluster has been modeled, analyzed and used for the calculations.

Binding of urea and thiourea with a barbiturate derivative: experimental and theoretical approach.

PubMed

Dixit, Namrata; Shukla, P K; Mishra, P C; Mishra, Lallan; Roesky, Herbert W

2010-01-14

A barbiturate derivative [1,5-dihydro-5-[5-pyrimidine-2,4(1H,3H)-dionyl]-2H-chromeno[2,3-d] pyrimidine-2,4(3H)-dione)] (L1) possesses functionalities complementary to amide and thioamide. Hence its binding with urea and thiourea, is monitored using UV-vis and fluorescence titrations as well as isothermal titration calorimetry (ITC) study. Theoretical studies on hydrogen-bonded complexes of L1-urea and L1-thiourea in the gas phase, aqueous, and DMSO medium are carried out using density functional theory (DFT) at the B3LYP/6-31G** level. The theoretical calculations support the experimental results.

Multireference Density Functional Theory with Generalized Auxiliary Systems for Ground and Excited States.

PubMed

Chen, Zehua; Zhang, Du; Jin, Ye; Yang, Yang; Su, Neil Qiang; Yang, Weitao

2017-09-21

To describe static correlation, we develop a new approach to density functional theory (DFT), which uses a generalized auxiliary system that is of a different symmetry, such as particle number or spin, from that of the physical system. The total energy of the physical system consists of two parts: the energy of the auxiliary system, which is determined with a chosen density functional approximation (DFA), and the excitation energy from an approximate linear response theory that restores the symmetry to that of the physical system, thus rigorously leading to a multideterminant description of the physical system. The electron density of the physical system is different from that of the auxiliary system and is uniquely determined from the functional derivative of the total energy with respect to the external potential. Our energy functional is thus an implicit functional of the physical system density, but an explicit functional of the auxiliary system density. We show that the total energy minimum and stationary states, describing the ground and excited states of the physical system, can be obtained by a self-consistent optimization with respect to the explicit variable, the generalized Kohn-Sham noninteracting density matrix. We have developed the generalized optimized effective potential method for the self-consistent optimization. Among options of the auxiliary system and the associated linear response theory, reformulated versions of the particle-particle random phase approximation (pp-RPA) and the spin-flip time-dependent density functional theory (SF-TDDFT) are selected for illustration of principle. Numerical results show that our multireference DFT successfully describes static correlation in bond dissociation and double bond rotation.

Diffusion Bonding of Silicon Carbide for a Micro-Electro-Mechanical Systems Lean Direct Injector

NASA Technical Reports Server (NTRS)

Halbig, Michael C.; Singh, Mrityunjay; Shpargel, Tarah P.; Kiser, James D.

2006-01-01

Robust approaches for joining silicon carbide (SiC) to silicon carbide sub-elements have been developed for a micro-electro-mechanical systems lean direct injector (MEMS LDI) application. The objective is to join SiC sub-elements to form a leak-free injector that has complex internal passages for the flow and mixing of fuel and air. Previous bonding technology relied upon silicate glass interlayers that were not uniform or leak free. In a newly developed joining approach, titanium foils and physically vapor deposited titanium coatings were used to form diffusion bonds between SiC materials during hot pressing. Microscopy results show the formation of well adhered diffusion bonds. Initial tests show that the bond strength is much higher than required for the component system. Benefits of the joining technology are fabrication of leak free joints with high temperature and mechanical capability.

A density functional theory model of mechanically activated silyl ester hydrolysis

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

Pill, Michael F.; Schmidt, Sebastian W.; Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098 Kiel

2014-01-28

To elucidate the mechanism of the mechanically activated dissociation of chemical bonds between carboxymethylated amylose (CMA) and silane functionalized silicon dioxide, we have investigated the dissociation kinetics of the bonds connecting CMA to silicon oxide surfaces with density functional calculations including the effects of force, solvent polarizability, and pH. We have determined the activation energies, the pre-exponential factors, and the reaction rate constants of candidate reactions. The weakest bond was found to be the silyl ester bond between the silicon and the alkoxy oxygen atom. Under acidic conditions, spontaneous proton addition occurs close to the silyl ester such that neutralmore » reactions become insignificant. Upon proton addition at the most favored position, the activation energy for bond hydrolysis becomes 31 kJ mol{sup −1}, which agrees very well with experimental observation. Heterolytic bond scission in the protonated molecule has a much higher activation energy. The experimentally observed bi-exponential rupture kinetics can be explained by different side groups attached to the silicon atom of the silyl ester. The fact that different side groups lead to different dissociation kinetics provides an opportunity to deliberately modify and tune the kinetic parameters of mechanically activated bond dissociation of silyl esters.« less

The effect of diffuse basis functions on valence bond structural weights

NASA Astrophysics Data System (ADS)

Galbraith, John Morrison; James, Andrew M.; Nemes, Coleen T.

2014-03-01

Structural weights and bond dissociation energies have been determined for H-F, H-X, and F-X molecules (-X = -OH, -NH2, and -CH3) at the valence bond self-consistent field (VBSCF) and breathing orbital valence bond (BOVB) levels of theory with the aug-cc-pVDZ and 6-31++G(d,p) basis sets. At the BOVB level, the aug-cc-pVDZ basis set yields a counterintuitive ordering of ionic structural weights when the initial heavy atom s-type basis functions are included. For H-F, H-OH, and F-X, the ordering follows chemical intuition when these basis functions are not included. These counterintuitive weights are shown to be a result of the diffuse polarisation function on one VB fragment being spatially located, in part, on the other VB fragment. Except in the case of F-CH3, this problem is corrected with the 6-31++G(d,p) basis set. The initial heavy atom s-type functions are shown to make an important contribution to the VB orbitals and bond dissociation energies and, therefore, should not be excluded. It is recommended to not use diffuse basis sets in valence bond calculations unless absolutely necessary. If diffuse basis sets are needed, the 6-31++G(d,p) basis set should be used with caution and the structural weights checked against VBSCF values which have been shown to follow the expected ordering in all cases.

Coulombic Models in Chemical Bonding.

ERIC Educational Resources Information Center

Sacks, Lawrence J.

1986-01-01

Describes a bonding theory which provides a framework for the description of a wide range of substances and provides quantitative information of remarkable accuracy with far less computational effort than that required of other approaches. Includes applications, such as calculation of bond energies of two binary hydrides (methane and diborane).…

Selective Loss of Cysteine Residues and Disulphide Bonds in a Potato Proteinase Inhibitor II Family

PubMed Central

Li, Xiu-Qing; Zhang, Tieling; Donnelly, Danielle

2011-01-01

Disulphide bonds between cysteine residues in proteins play a key role in protein folding, stability, and function. Loss of a disulphide bond is often associated with functional differentiation of the protein. The evolution of disulphide bonds is still actively debated; analysis of naturally occurring variants can promote understanding of the protein evolutionary process. One of the disulphide bond-containing protein families is the potato proteinase inhibitor II (PI-II, or Pin2, for short) superfamily, which is found in most solanaceous plants and participates in plant development, stress response, and defence. Each PI-II domain contains eight cysteine residues (8C), and two similar PI-II domains form a functional protein that has eight disulphide bonds and two non-identical reaction centres. It is still unclear which patterns and processes affect cysteine residue loss in PI-II. Through cDNA sequencing and data mining, we found six natural variants missing cysteine residues involved in one or two disulphide bonds at the first reaction centre. We named these variants Pi7C and Pi6C for the proteins missing one or two pairs of cysteine residues, respectively. This PI-II-7C/6C family was found exclusively in potato. The missing cysteine residues were in bonding pairs but distant from one another at the nucleotide/protein sequence level. The non-synonymous/synonymous substitution (Ka/Ks) ratio analysis suggested a positive evolutionary gene selection for Pi6C and various Pi7C. The selective deletion of the first reaction centre cysteine residues that are structure-level-paired but sequence-level-distant in PI-II illustrates the flexibility of PI-II domains and suggests the functionality of their transient gene versions during evolution. PMID:21494600

Novel Bonding Technology for Hermetically Sealed Silicon Micropackage

NASA Astrophysics Data System (ADS)

Lee, Duck-Jung; Ju, Byeong-Kwon; Choi, Woo-Beom; Jeong, Jee-Won; Lee, Yun-Hi; Jang, Jin; Lee, Kwang-Bae; Oh, Myung-Hwan

1999-01-01

We performed glass-to-silicon bonding and fabricated a hermetically sealed silicon wafer using silicon direct bonding followed by anodic bonding (SDAB). The hydrophilized glass and silicon wafers in solution were dried and initially bonded in atmosphere as in the silicon direct bonding (SDB) process, but annealing at high temperature was not performed. Anodic bonding was subsequently carried out for the initially bonded specimens. Then the wafer pairs bonded by the SDAB method were different from those bonded by the anodic bonding process only. The effects of the bonding process on the bonded area and tensile strength were investigated as functions of bonding temperature and voltage. Using scanning electron microscopy (SEM), the cross-sectional view of the bonded interface region was observed. In order to investigate the migration of the sodium ions in the bonding process, the concentration of the bonded glass was compared with that of standard glass. The specimen bonded using the SDAB process had higher efficiency than that using the anodic bonding process only.

Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy

DOE PAGES

Mara, Michael W.; Hadt, Ryan G.; Reinhard, Marco Eli; ...

2017-06-23

The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. As a result, the 4 kcal/molmore » is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.« less

Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy

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

Mara, Michael W.; Hadt, Ryan G.; Reinhard, Marco Eli

The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. As a result, the 4 kcal/molmore » is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.« less

Theoretical electrical conductivity of hydrogen-bonded benzamide-derived molecules and single DNA bases.

PubMed

Chen, Xiang

2013-09-01

A benzamide molecule is used as a "reader" molecule to form hydrogen bonds with five single DNA bases, i.e., four normal single DNA bases A,T,C,G and one for 5methylC. The whole molecule is then attached to the gold surface so that a meta-molecule junction is formed. We calculate the transmission function and conductance for the five metal-molecule systems, with the implementation of density functional theory-based non-equilibrium Green function method. Our results show that each DNA base exhibits a unique conductance and most of them are on the pS level. The distinguishable conductance of each DNA base provides a way for the fast sequencing of DNA. We also investigate the dependence of conductivity of such a metal-molecule system on the hydrogen bond length between the "reader" molecule and DNA base, which shows that conductance follows an exponential decay as the hydrogen bond length increases, i.e., the conductivity is highly sensitive to the change in hydrogen bond length.

Ab initio calculation of resonant Raman intensities of transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Miranda, Henrique; Reichardt, Sven; Molina-Sanchez, Alejandro; Wirtz, Ludger

Raman spectroscopy is used to characterize optical and vibrational properties of materials. Its computational simulation is important for the interpretation of experimental results. Two approaches are the bond polarizability model and density functional perturbation theory. However, both are known to not capture resonance effects. These resonances and quantum interference effects are important to correctly reproduce the intensities as a function of laser energy as, e.g., reported for the case of multi-layer MoTe21.We present two fully ab initio approaches that overcome this limitation. In the first, we calculate finite difference derivatives of the dielectric susceptibility with the phonon displacements2. In the second we calculate electron-light and electron-phonon matrix elements from density functional theory and use them to evaluate expressions for the Raman intensity derived from time-dependent perturbation theory. These expressions are implemented in a computer code that performs the calculations as a post-processing step. We compare both methods and study the case of triple-layer MoTe2. Luxembourg National Research Fund (FNR).

Synthesis of antiviral tetrahydrocarbazole derivatives by photochemical and acid-catalyzed C-H functionalization via intermediate peroxides (CHIPS).

PubMed

Gulzar, Naeem; Klussmann, Martin

2014-06-20

The direct functionalization of C-H bonds is an important and long standing goal in organic chemistry. Such transformations can be very powerful in order to streamline synthesis by saving steps, time and material compared to conventional methods that require the introduction and removal of activating or directing groups. Therefore, the functionalization of C-H bonds is also attractive for green chemistry. Under oxidative conditions, two C-H bonds or one C-H and one heteroatom-H bond can be transformed to C-C and C-heteroatom bonds, respectively. Often these oxidative coupling reactions require synthetic oxidants, expensive catalysts or high temperatures. Here, we describe a two-step procedure to functionalize indole derivatives, more specifically tetrahydrocarbazoles, by C-H amination using only elemental oxygen as oxidant. The reaction uses the principle of C-H functionalization via Intermediate PeroxideS (CHIPS). In the first step, a hydroperoxide is generated oxidatively using visible light, a photosensitizer and elemental oxygen. In the second step, the N-nucleophile, an aniline, is introduced by Brønsted-acid catalyzed activation of the hydroperoxide leaving group. The products of the first and second step often precipitate and can be conveniently filtered off. The synthesis of a biologically active compound is shown.

Bond breaking in epoxy systems: A combined QM/MM approach

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

Barr, Stephen A.; Ecker, Allison M.; Berry, Rajiv J., E-mail: Rajiv.Berry@us.af.mil

2016-06-28

A novel method to combine quantum mechanics (QM) and molecular mechanics has been developed to accurately and efficiently account for covalent bond breaking in polymer systems under high strain without the use of predetermined break locations. Use of this method will provide a better fundamental understanding of the mechano-chemical origins of fracture in thermosets. Since classical force fields cannot accurately account for bond breaking, and QM is too demanding to simulate large systems, a hybrid approach is required. In the method presented here, strain is applied to the system using a classical force field, and all bond lengths are monitored.more » When a bond is stretched past a threshold value, a zone surrounding the bond is used in a QM energy minimization to determine which, if any, bonds break. The QM results are then used to reconstitute the system to continue the classical simulation at progressively larger strain until another QM calculation is triggered. In this way, a QM calculation is only computed when and where needed, allowing for efficient simulations. A robust QM method for energy minimization has been determined, as well as appropriate values for the QM zone size and the threshold bond length. Compute times do not differ dramatically from classical molecular mechanical simulations.« less

Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations

NASA Astrophysics Data System (ADS)

Srivastava, Abhinav; Debnath, Ananya

2018-03-01

Dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer are investigated using an all atom molecular dynamics simulation. Based upon the geometric criteria, continuously residing interface water molecules which form hydrogen bonds solely among themselves and then concertedly hydrogen bonded to carbonyl, phosphate, and glycerol head groups of DMPC are identified. The interface water hydrogen bonded to lipids shows slower relaxation rates for translational and rotational dynamics compared to that of the bulk water and is found to follow sub-diffusive and non-diffusive behaviors, respectively. The mean square displacements and the reorientational auto-correlation functions are slowest for the interfacial waters hydrogen bonded to the carbonyl oxygen since these are buried deep in the hydrophobic core among all interfacial water studied. The intermittent hydrogen bond auto-correlation functions are calculated, which allows breaking and reformations of the hydrogen bonds. The auto-correlation functions for interfacial hydrogen bonded networks develop humps during a transition from cage-like motion to eventual power law behavior of t-3/2. The asymptotic t-3/2 behavior indicates translational diffusion dictated dynamics during hydrogen bond breaking and formation irrespective of the nature of the chemical confinement. Employing reactive flux correlation analysis, the forward rate constant of hydrogen bond breaking and formation is calculated which is used to obtain Gibbs energy of activation of the hydrogen bond breaking. The relaxation rates of the networks buried in the hydrophobic core are slower than the networks near the lipid-water interface which is again slower than bulk due to the higher Gibbs energy of activation. Since hydrogen bond breakage follows a translational diffusion dictated mechanism, chemically confined hydrogen bond networks need an activation energy to diffuse through water depleted hydrophobic environments. Our calculations reveal that the slow relaxation rates of interfacial waters in the vicinity of lipids are originated from the chemical confinement of concerted hydrogen bond networks. The analysis suggests that the networks in the hydration layer of membranes dynamically facilitate the water mediated lipid-lipid associations which can provide insights on the thermodynamic stability of soft interfaces relevant to biological systems in the future.

Thermally activated rotational disorder in CaMoO 4 nanocrystals

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

Culver, Sean P.; Brutchey, Richard L.

2016-04-12

In this study, a dual-space approach, combining Rietveld and pair distribution function (PDF) analyses, has been applied to temperature-dependent synchrotron X-ray total scattering data collected on vapor diffusion sol–gel derived CaMoO 4 nanocrystals. A sharp transition in Ca–O bond distances in the range of 151–163 K was identified by PDF analysis, which is attributed to the thermal activation of rotational disorder associated with the rigid MoO 4 tetrahedra.

A strategy for position-selective epoxidation of polyprenols.

PubMed

Gnanadesikan, Vijay; Corey, E J

2008-06-25

An effective strategy has been developed for the efficient site-selective epoxidation of poylolefinic isoprenoid alcohols, based on the use of an internal control element for intramolecular reaction. The approach is illustrated by application to a series of polyisoprenoid alcohols (polyprenols) at substrate concentration of 0.5 mM. With polyprenol substrates having the hydroxyl function at one terminus, the internal epoxidation can be directed at the double bond of the polyprenol, which is either four or five away from the terminal hydroxyprenyl subunit.

NDT evaluation of long-term bond durability of CFRP-structural systems applied to RC highway bridges

NASA Astrophysics Data System (ADS)

Crawford, Kenneth C.

2016-06-01

The long-term durability of CFRP structural systems applied to reinforced-concrete (RC) highway bridges is a function of the system bond behavior over time. The sustained structural load performance of strengthened bridges depends on the carbon fiber-reinforced polymer (CFRP) laminates remaining 100 % bonded to concrete bridge members. Periodic testing of the CFRP-concrete bond condition is necessary to sustain load performance. The objective of this paper is to present a non-destructive testing (NDT) method designed to evaluate the bond condition and long-term durability of CFRP laminate (plate) systems applied to RC highway bridges. Using the impact-echo principle, a mobile mechanical device using light impact hammers moving along the length of a bonded CFRP plate produces unique acoustic frequencies which are a function of existing CFRP plate-concrete bond conditions. The purpose of this method is to test and locate CFRP plates de-bonded from bridge structural members to identify associated deterioration in bridge load performance. Laboratory tests of this NDT device on a CFRP plate bonded to concrete with staged voids (de-laminations) produced different frequencies for bonded and de-bonded areas of the plate. The spectra (bands) of frequencies obtained in these tests show a correlation to the CFRP-concrete bond condition and identify bonded and de-bonded areas of the plate. The results of these tests indicate that this NDT impact machine, with design improvements, can potentially provide bridge engineers a means to rapidly evaluate long lengths of CFRP laminates applied to multiple highway bridges within a national transportation infrastructure.

Transition from metal-ligand bonding to halogen bonding involving a metal as halogen acceptor a study of Cu, Ag, Au, Pt, and Hg complexes

NASA Astrophysics Data System (ADS)

Oliveira, Vytor; Cremer, Dieter

2017-08-01

Utilizing all-electron Dirac-exact relativistic calculations with the Normalized Elimination of the Small Component (NESC) method and the local vibrational mode approach, the transition from metal-halide to metal halogen bonding is determined for Au-complexes interacting with halogen-donors. The local stretching force constants of the metal-halogen interactions reveal a smooth transition from weak non-covalent halogen bonding to non-classical 3-center-4-electron bonding and finally covalent metal-halide bonding. The strongest halogen bonds are found for dialkylaurates interacting with Cl2 or FCl. Differing trends in the intrinsic halogen-metal bond strength, the binding energy, and the electrostatic potential are explained.

Long Life, Low Power, Multi-Cell Battery

DTIC Science & Technology

2010-10-28

complementary glass structures that provide for the containment walls that hold the electrolyte. B. Major task will involve the use...of an anodic bonding approach to fuse the silicon substrate containing the micro channels to the glass grid wall structures described above...Completion August 2010 Task B. completed, anodic bonding approach used on top glass and silicon layers

Irreversible bonding of polyimide and polydimethylsiloxane (PDMS) based on a thiol-epoxy click reaction

NASA Astrophysics Data System (ADS)

Hoang, Michelle V.; Chung, Hyun-Joong; Elias, Anastasia L.

2016-10-01

Polyimide is one of the most popular substrate materials for the microfabrication of flexible electronics, while polydimethylsiloxane (PDMS) is the most widely used stretchable substrate/encapsulant material. These two polymers are essential in fabricating devices for microfluidics, bioelectronics, and the internet of things; bonding these materials together is a crucial challenge. In this work, we employ click chemistry at room temperature to irreversibly bond polyimide and PDMS through thiol-epoxy bonds using two different methods. In the first method, we functionalize the surfaces of the PDMS and polyimide substrates with mercaptosilanes and epoxysilanes, respectively, for the formation of a thiol-epoxy bond in the click reaction. In the second method, we functionalize one or both surfaces with mercaptosilane and introduce an epoxy adhesive layer between the two surfaces. When the surfaces are bonded using the epoxy adhesive without any surface functionalization, an extremely small peel strength (<0.01 N mm-1) is measured with a peel test, and adhesive failure occurs at the PDMS surface. With surface functionalization, however, remarkably higher peel strengths of ~0.2 N mm-1 (method 1) and  >0.3 N mm-1 (method 2) are observed, and failure occurs by tearing of the PDMS layer. We envision that the novel processing route employing click chemistry can be utilized in various cases of stretchable and flexible device fabrication.

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.

PubMed

Cerný, Jirí; Hobza, Pavel

2005-04-21

The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

Grism manufacturing by low temperature mineral bonding

NASA Astrophysics Data System (ADS)

Kalkowski, G.; Grabowski, K.; Harnisch, G.; Flügel-Paul, T.; Zeitner, U.; Risse, S.

2017-09-01

By uniting a grating with a prism to a GRISM compound, the optical characteristics of diffractive and refractive elements can be favorably combined to achieve outstanding spectral resolution features. Ruling the grating structure into the prism surface is common for wavelengths around 1 μm and beyond, while adhesive bonding of two separate parts is generally used for shorter wavelengths and finer structures. We report on a manufacturing approach for joining the corresponding glass elements by the technology of hydrophilic direct bonding. This allows to manufacture the individual parts separately and subsequently combine them quasimonolithically by generating stiff and durable bonds of vanishing thickness, high strength and excellent transmission. With this approach for GRISM bonding, standard direct-write- or mask-lithography equipment may be used for the fabrication of the grating structure and the drawbacks of adhesive bonding (thermal mismatch, creep, aging) are avoided. The technology of hydrophilic bonding originates from "classical" optical contacting [1], but has been much improved and perfected during the last decades in the context of 3-dimensinal stacking Si-wafers for microelectronic applications [2]. It provides joins through covalent bonds of the Si-O-Si type at the nanometer scale, i.e. the elementary bond type in many minerals and glasses. The mineral nature of the bond is perfectly adapted to most optical materials and the extremely thin bonding layers generated with this technology are well suited for transmission optics. Creeping under mechanical load, as commonly observed with adhesive bonding, is not an issue. With respect to diffusion bonding, which operates at rather high temperatures close to the glass transition or crystal melting point, hydrophilic bonding is a low temperature process that needs only moderate heating. This facilitates provision of handling and alignment means for the individual parts during the set-up stages and greatly eases joining optical materials of different thermal expansion. The technology has been successfully used in the past for bonding various glasses as well as crystalline optical materials [3, 4]. Here we will focus on bonding prisms elements and binary gratings of fused silica with and without coatings at the bonding interface. Further, preliminary results on bonding prism-grating-prism (PGP) combinations will be presented.

Potential surfaces for O atom-polymer reactions

NASA Technical Reports Server (NTRS)

Laskowski, B. C.; Jaffe, R. L.

1987-01-01

Ab initio quantum chemistry methods are used to study the energetics of interactions of O atoms with organic compounds. Polyethylene (CH2)n has been chosen as the model system to study the interactions of O(3P) and O(1D) atoms with polymers. In particular, H abstraction is investigated and polyethylene is represented by a C3 (propane) oligomeric model. The gradient method, as implemented in the GRADSCF package of programs, is used to determine the geometries and energies of products and reactants. The saddle point, barrier geometry is determined by minimizing the squares of the gradients of the potential with respect to the internal coordinates. To correctly describe the change in bonding during the reaction at least a two configuration MCSCF (multiconfiguration self consistent field) or GVB (generalized valence bond) wave function has to be used. Basis sets include standard Pople and Dunning sets, however, increased with polarization functions and diffuse p functions on both the C and O atoms. The latter is important due to the O(-) character of the wave function at the saddle point and products. Normal modes and vibrational energy levels are given for the reactants, saddle points and products. Finally, quantitative energetics are obtained by implementing a small CAS (complete active space) approach followed by limited configuration interaction (CI) calculations. Comparisons are made with available experimental data.

A polarizable dipole-dipole interaction model for evaluation of the interaction energies for N-H···O=C and C-H···O=C hydrogen-bonded complexes.

PubMed

Li, Shu-Shi; Huang, Cui-Ying; Hao, Jiao-Jiao; Wang, Chang-Sheng

2014-03-05

In this article, a polarizable dipole-dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen-bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N-H, C=O, and C-H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole-dipole interaction model to a series of hydrogen-bonded complexes containing the N-H···O=C and C-H···O=C hydrogen bonds, such as simple amide-amide dimers, base-base dimers, peptide-base dimers, and β-sheet models. We find that a simple two-term function, only containing the permanent dipole-dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6-31G(d) method, whereas the high-quality counterpoise-corrected (CP-corrected) MP2/aug-cc-pVTZ interaction energies for the hydrogen-bonded complexes can be well-reproduced by a four-term function which involves the permanent dipole-dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole-dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen-bonded complexes are further discussed. Copyright © 2013 Wiley Periodicals, Inc.

A Novel Method to Quantify Soil Aggregate Stability by Measuring Aggregate Bond Energies

NASA Astrophysics Data System (ADS)

Efrat, Rachel; Rawlins, Barry G.; Quinton, John N.; Watts, Chris W.; Whitmore, Andy P.

2016-04-01

Soil aggregate stability is a key indicator of soil quality because it controls physical, biological and chemical functions important in cultivated soils. Micro-aggregates are responsible for the long term sequestration of carbon in soil, therefore determine soils role in the carbon cycle. It is thus vital that techniques to measure aggregate stability are accurate, consistent and reliable, in order to appropriately manage and monitor soil quality, and to develop our understanding and estimates of soil as a carbon store to appropriately incorporate in carbon cycle models. Practices used to assess the stability of aggregates vary in sample preparation, operational technique and unit of results. They use proxies and lack quantification. Conflicting results are therefore drawn between projects that do not provide methodological or resultant comparability. Typical modern stability tests suspend aggregates in water and monitor fragmentation upon exposure to an un-quantified amount of ultrasonic energy, utilising a laser granulometer to measure the change in mean weight diameter. In this project a novel approach has been developed based on that of Zhu et al., (2009), to accurately quantify the stability of aggregates by specifically measuring their bond energies. The bond energies are measured operating a combination of calorimetry and a high powered ultrasonic probe, with computable output function. Temperature change during sonication is monitored by an array of probes which enables calculation of the energy spent heating the system (Ph). Our novel technique suspends aggregates in heavy liquid lithium heteropolytungstate, as opposed to water, to avoid exposing aggregates to an immeasurable disruptive energy source, due to cavitation, collisions and clay swelling. Mean weight diameter is measured by a laser granulometer to monitor aggregate breakdown after successive periods of calculated ultrasonic energy input (Pi), until complete dispersion is achieved and bond energy (Pb; input energy used in aggregate breakdown) can be calculated by the following equation: ΣPi - Ph = Pb The novel technique was tested by comparing the bond energies measured from a series of soil aggregates sampled from different land management histories, to the samples corresponding stability measurement obtained from standard modern stability tests. The effectiveness of the heavy liquid as a suspension (as opposed to water) was evaluated by comparing the bond energies of samples measured in both suspensions. Our results determine i) how disruptive water is in aggregate stability tests, ii) how accurate and representative standard aggregate stability tests are, and iii) how bond strength varies depending on land use. Keywords: Aggregate; Bond; Fragmentation; Soil; Sonication; Stability References: Zhu, Z. L., Minasny, B. & Field D. J. 2009. Measurement of aggregate bond energy using ultrasonic dispersion. European Journal of Soil Science, 60, 695-705

Photoresponsive liquid crystalline epoxy networks with shape memory behavior and dynamic ester bonds

DOE PAGES

Rios, Orlando; Chen, Jihua; Li, Yuzhan; ...

2016-06-01

Functional polymers are intelligent materials that can respond to a variety of external stimuli. However, these materials have not yet found widespread real world applications because of the difficulties in fabrication and the limited number of functional building blocks that can be incorporated into a material. Here, we demonstrate a simple route to incorporate three functional building blocks (azobenzene chromophores, liquid crystals, and dynamic covalent bonds) into an epoxy-based liquid crystalline network (LCN), in which an azobenzene-based epoxy monomer is polymerized with an aliphatic dicarboxylic acid to create exchangeable ester bonds that can be thermally activated. Lastly, all three functionalmore » building blocks exhibited good compatibility, and the resulting materials exhibits various photomechanical, shape memory, and self-healing properties because of the azobenzene molecules, liquid crystals, and dynamic ester bonds, respectively.« less

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.

Total synthesis of feglymycin based on a linear/convergent hybrid approach using micro-flow amide bond formation

NASA Astrophysics Data System (ADS)

Fuse, Shinichiro; Mifune, Yuto; Nakamura, Hiroyuki; Tanaka, Hiroshi

2016-11-01

Feglymycin is a naturally occurring, anti-HIV and antimicrobial 13-mer peptide that includes highly racemizable 3,5-dihydroxyphenylglycines (Dpgs). Here we describe the total synthesis of feglymycin based on a linear/convergent hybrid approach. Our originally developed micro-flow amide bond formation enabled highly racemizable peptide chain elongation based on a linear approach that was previously considered impossible. Our developed approach will enable the practical preparation of biologically active oligopeptides that contain highly racemizable amino acids, which are attractive drug candidates.

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.

Bond-Energy and Surface-Energy Calculations in Metals

ERIC Educational Resources Information Center

Eberhart, James G.; Horner, Steve

2010-01-01

A simple technique appropriate for introductory materials science courses is outlined for the calculation of bond energies in metals from lattice energies. The approach is applied to body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal-closest-packed (hcp) metals. The strength of these bonds is tabulated for a variety metals and is…

Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism

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

Camilloni, Carlo; Sahakyan, Aleksander B.; Holliday, Michael

2014-07-15

Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions1-3. Different families of enzymes, known as peptidyl-prolyl isomerases (PPIases), catalyse this reaction, which involves the interconversion between the cis and trans isomers of the Nterminal amide bond of the amino acid proline2,3. A complete description of the mechanisms by which these enzymes function, however, has remained elusive. Here, we show that cyclophilin A, one of the most common PPIases4, provides a catalytic environment that acts on the substrate through an electrostatic lever mechanism. In this mechanism, themore » electrostatic field in the catalytic site turns the electric dipole associated with the carboxylic group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. This mechanism resulted from the analysis of an ensemble of conformations populated by cyclophilin A during the enzymatic reaction using a combination of NMR measurements, molecular dynamics simulations and density functional theory calculations. We anticipate that this approach will be helpful in elucidating whether the electrostatic lever mechanism that we describe is common to other PPIases, and more generally to characterise other enzymatic processes.« less

Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism

PubMed Central

Camilloni, Carlo; Sahakyan, Aleksandr B.; Holliday, Michael J.; Isern, Nancy G.; Zhang, Fengli; Eisenmesser, Elan Z.; Vendruscolo, Michele

2014-01-01

Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions. Different families of enzymes, known as “peptidyl-prolyl isomerases” (PPIases), catalyze this reaction, which involves the interconversion between the cis and trans isomers of the N-terminal amide bond of the amino acid proline. However, complete descriptions of the mechanisms by which these enzymes function have remained elusive. We show here that cyclophilin A, one of the most common PPIases, provides a catalytic environment that acts on the substrate through an electrostatic handle mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carbonyl group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. We identified this mechanism using a combination of NMR measurements, molecular dynamics simulations, and density functional theory calculations to simultaneously determine the cis-bound and trans-bound conformations of cyclophilin A and its substrate as the enzymatic reaction takes place. We anticipate that this approach will be helpful in elucidating whether the electrostatic handle mechanism that we describe here is common to other PPIases and, more generally, in characterizing other enzymatic processes. PMID:24982184

Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism.

PubMed

Camilloni, Carlo; Sahakyan, Aleksandr B; Holliday, Michael J; Isern, Nancy G; Zhang, Fengli; Eisenmesser, Elan Z; Vendruscolo, Michele

2014-07-15

Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions. Different families of enzymes, known as "peptidyl-prolyl isomerases" (PPIases), catalyze this reaction, which involves the interconversion between the cis and trans isomers of the N-terminal amide bond of the amino acid proline. However, complete descriptions of the mechanisms by which these enzymes function have remained elusive. We show here that cyclophilin A, one of the most common PPIases, provides a catalytic environment that acts on the substrate through an electrostatic handle mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carbonyl group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. We identified this mechanism using a combination of NMR measurements, molecular dynamics simulations, and density functional theory calculations to simultaneously determine the cis-bound and trans-bound conformations of cyclophilin A and its substrate as the enzymatic reaction takes place. We anticipate that this approach will be helpful in elucidating whether the electrostatic handle mechanism that we describe here is common to other PPIases and, more generally, in characterizing other enzymatic processes.

Multireference second order perturbation theory with a simplified treatment of dynamical correlation.

PubMed

Xu, Enhua; Zhao, Dongbo; Li, Shuhua

2015-10-13

A multireference second order perturbation theory based on a complete active space configuration interaction (CASCI) function or density matrix renormalized group (DMRG) function has been proposed. This method may be considered as an approximation to the CAS/A approach with the same reference, in which the dynamical correlation is simplified with blocked correlated second order perturbation theory based on the generalized valence bond (GVB) reference (GVB-BCPT2). This method, denoted as CASCI-BCPT2/GVB or DMRG-BCPT2/GVB, is size consistent and has a similar computational cost as the conventional second order perturbation theory (MP2). We have applied it to investigate a number of problems of chemical interest. These problems include bond-breaking potential energy surfaces in four molecules, the spectroscopic constants of six diatomic molecules, the reaction barrier for the automerization of cyclobutadiene, and the energy difference between the monocyclic and bicyclic forms of 2,6-pyridyne. Our test applications demonstrate that CASCI-BCPT2/GVB can provide comparable results with CASPT2 (second order perturbation theory based on the complete active space self-consistent-field wave function) for systems under study. Furthermore, the DMRG-BCPT2/GVB method is applicable to treat strongly correlated systems with large active spaces, which are beyond the capability of CASPT2.

A Report of Undergraduates' Bonding Misconceptions.

ERIC Educational Resources Information Center

Nicoll, Gayle

2001-01-01

Describes misconceptions related to electronegativity, bonding, geometry, and microscopic representations that undergraduate students hold. Investigates the stability of misconceptions as a function of educational level, indicating that some students' misconceptions relating to bonding are resistant to change despite increased chemistry education.…

A Palladium Iodide-Catalyzed Oxidative Aminocarbonylation-Heterocyclization Approach to Functionalized Benzimidazoimidazoles.

PubMed

Veltri, Lucia; Giofrè, Salvatore V; Devo, Perry; Romeo, Roberto; Dobbs, Adrian P; Gabriele, Bartolo

2018-02-02

A novel carbonylative approach to the synthesis of functionalized 1H-benzo[d]imidazo[1,2-a]imidazoles is presented. The method consists of the oxidative aminocarbonylation of N-substituted-1-(prop-2-yn-1-yl)-1H-benzo[d]imidazol-2-amines, carried out in the presence of secondary nucleophilic amines, to give the corresponding alkynylamide intermediates, followed by in situ conjugated addition and double-bond isomerization, to give 2-(1-alkyl-1H-benzo[d]imidazo[1,2-a]imidazol-2-yl)acetamides. Products were obtained in good to excellent yields (64-96%) and high turnover numbers (192-288 mol of product per mol of catalyst) under relatively mild conditions (100 °C under 20 atm of a 4:1 mixture of CO-air), using a simple catalytic system, consisting of PdI 2 (0.33 mol %) in conjunction with KI (0.33 equiv).

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

Yu, Liang; Abild-Pedersen, Frank

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. Here, we have applied this approach together withmore » linear scaling of adsorption energies to obtain the energetics of the NH 3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. Moreover, this information is used to establish a microkinetic model for the formation of N 2 and H 2, thus providing insight into the components of the reaction that determines the activity.« less

Integrated microsystems packaging approach with LCP

NASA Astrophysics Data System (ADS)

Jaynes, Paul; Shacklette, Lawrence W.

2006-05-01

Within the government communication market there is an increasing push to further miniaturize systems with the use of chip-scale packages, flip-chip bonding, and other advances over traditional packaging techniques. Harris' approach to miniaturization includes these traditional packaging advances, but goes beyond this level of miniaturization by combining the functional and structural elements of a system, thus creating a Multi-Functional Structural Circuit (MFSC). An emerging high-frequency, near hermetic, thermoplastic electronic substrate material, Liquid Crystal Polymer (LCP), is the material that will enable the combination of the electronic circuit and the physical structure of the system. The first embodiment of this vision for Harris is the development of a battlefield acoustic sensor module. This paper will introduce LCP and its advantages for MFSC, present an example of the work that Harris has performed, and speak to LCP MFSCs' potential benefits to miniature communications modules and sensor platforms.

First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces.

PubMed

Kharche, Neerav; Muckerman, James T; Hybertsen, Mark S

2014-10-24

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The  GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b1 energy level in water. The application to the specific cases of nonpolar (101¯0) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. These effects contribute up to 0.5 eV.

Study of the physical properties of Ge-S-Ga glassy alloy

NASA Astrophysics Data System (ADS)

Rana, Anjli; Sharma, Raman

2018-05-01

In the present work, we have studied the effect of Ga doping on the physical properties of Ge20S80-xGax glassy alloy. The basic physical parameters which have important role in determining the structure and strength of the material viz. average coordination number, lone-pair electrons, mean bond energy, glass transition temperature, electro negativity, probabilities for bond distribution and cohesive energy have been computed theoretically for Ge-S-Ga glassy alloy. Here, the glass transition temperature and mean bond energy have been investigated using the Tichy-Ticha approach. The cohesive energy has been calculated by using chemical bond approach (CBA) method. It has been found that while average coordination number increases, all the other parameters decrease with the increase in Ga content in Ge-S-Ga system.

Enhanced stab resistance of armor composites with functionalized silica nanoparticles

NASA Astrophysics Data System (ADS)

Mahfuz, Hassan; Clements, Floria; Rangari, Vijaya; Dhanak, Vinod; Beamson, Graham

2009-03-01

Traditionally shear thickening fluid (STF) reinforced with Kevlar has been used to develop flexible armor. At the core of the STF-Kevlar composites is a mixture of polyethylene glycol (PEG) and silica particles. This mixture is often known as STF and is consisted of approximately 45 wt % PEG and 55 wt % silica. During rheological tests, STF shows instantaneous spike in viscosity above a critical shear rate. Fabrication of STF-Kevlar composites requires preparation of STF, dilution with ethanol, and then impregnation with Kevlar. In the current approach, nanoscale silica particles were dispersed directly into a mixture of PEG and ethanol through a sonic cavitation process. Two types of silica nanoparticles were used in the investigation: 30 nm crystalline silica and 7 nm amorphous silica. The admixture was then reinforced with Kevlar fabric to produce flexible armor composites. In the next step, silica particles are functionalized with a silane coupling agent to enhance bonding between silica and PEG. The performance of the resulting armor composites improved significantly. As evidenced by National Institute of Justice spike tests, the energy required for zero-layer penetration (i.e., no penetration) jumped twofold: from 12 to 25 J cm2/g. The source of this improvement has been traced to the formation of siloxane (Si-O-Si) bonds between silica and PEG and superior coating of Kevlar filaments with particles. Fourier transform infrared, x-ray photoemission spectroscopy, and scanning electron microscopy studies were performed to examine chemical bonds, elemental composition, and particle dispersion responsible for such improvement. In summary, our experiments have demonstrated that functionalization of silica particles followed by direct dispersion into PEG resulted in superior Kevlar composites having much higher spike resistance.

Carboxylate-assisted ruthenium-catalyzed alkyne annulations by C-H/Het-H bond functionalizations.

PubMed

Ackermann, Lutz

2014-02-18

To improve the atom- and step-economy of organic syntheses, researchers would like to capitalize upon the chemistry of otherwise inert carbon-hydrogen (C-H) bonds. During the past decade, remarkable progress in organometallic chemistry has set the stage for the development of increasingly viable metal catalysts for C-H bond activation reactions. Among these methods, oxidative C-H bond functionalizations are particularly attractive because they avoid the use of prefunctionalized starting materials. For example, oxidative annulations that involve sequential C-H and heteroatom-H bond cleavages allow for the modular assembly of regioselectively decorated heterocycles. These structures serve as key scaffolds for natural products, functional materials, crop protecting agents, and drugs. While other researchers have devised rhodium or palladium complexes for oxidative alkyne annulations, my laboratory has focused on the application of significantly less expensive, yet highly selective ruthenium complexes. This Account summarizes the evolution of versatile ruthenium(II) complexes for annulations of alkynes via C-H/N-H, C-H/O-H, or C-H/N-O bond cleavages. To achieve selective C-H bond functionalizations, we needed to understand the detailed mechanism of the crucial C-H bond metalation with ruthenium(II) complexes and particularly the importance of carboxylate assistance in this process. As a consequence, our recent efforts have resulted in widely applicable methods for the versatile preparation of differently decorated arenes and heteroarenes, providing access to among others isoquinolones, 2-pyridones, isoquinolines, indoles, pyrroles, or α-pyrones. Most of these reactions used Cu(OAc)2·H2O, which not only acted as the oxidant but also served as the essential source of acetate for the carboxylate-assisted ruthenation manifold. Notably, the ruthenium(II)-catalyzed oxidative annulations also occurred under an ambient atmosphere of air with cocatalytic amounts of Cu(OAc)2·H2O. Moreover, substrates displaying N-O bonds served as "internal oxidants" for the syntheses of isoquinolones and isoquinolines. Detailed experimental mechanistic studies have provided strong support for a catalytic cycle that relies on initial carboxylate-assisted C-H bond ruthenation, followed by coordinative insertion of the alkyne, reductive elimination, and reoxidation of the thus formed ruthenium(0) complex.

Density Functionals of Chemical Bonding

PubMed Central

Putz, Mihai V.

2008-01-01

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. PMID:19325846

Hydroxylation of organic polymer surface: method and application.

PubMed

Yang, Peng; Yang, Wantai

2014-03-26

It may be hardly believable that inert C-H bonds on a polymeric material surface could be quickly and efficiently transformed into C-OH by a simple and mild way. Thanks to the approaches developed recently, it is now possible to transform surface H atoms of a polymeric substrate into monolayer OH groups by a simple/mild photochemical reaction. Herein the method and application of this small-molecular interfacial chemistry is highlighted. The existence of hydroxyl groups on material surfaces not only determines the physical and chemical properties of materials but also provides effective reaction sites for postsynthetic sequential modification to fulfill the requirements of various applications. However, organic synthetic materials based on petroleum, especially polyolefins comprise mainly C and H atoms and thus present serious surface problems due to low surface energy and inertness in reactivity. These limitations make it challenging to perform postsynthetic surface sequential chemical derivatization toward enhanced functionalities and properties and also cause serious interfacial problems when bonding or integrating polymer substrates with natural or inorganic materials. Polymer surface hydroxylation based on direct conversion of C-H bonds on polymer surfaces is thus of significant importance for academic and practical industrial applications. Although highly active research results have reported on small-molecular C-H bond activation in solution (thus homogeneous), most of them, featuring the use of a variety of transition metals as catalysts, present a slow reaction rate, a low atom economy and an obvious environmental pollution. In sharp contrast to these conventional C-H activation strategies, the present Spotlight describes a universal confined photocatalytic oxidation (CPO) system that is able to directly convert polymer surface C-H bonds to C-OSO3(-) and, subsequently, to C-OH through a simple hydrolysis. Generally speaking, these newly implanted hydroxyl groups preserve their own reactivity toward other complementary compounds, thus creating a novel base with distinct surface properties. Thanks to this functionalized platform, a wide range of organic, inorganic and metal materials have been attached to conventional organic polymer substrates through the rational engineering of surface molecular templates from small functional groups to macromolecules. It is expected that the proposed novel CPO method and its versatile usages in advanced material applications will offer new opportunities for a variety of scientific communities, especially for those working on surface/interface modulation.

Self-reported emotional and behavioral symptoms, parent-adolescent bonding and family functioning in clinically referred adolescent offspring of Croatian PTSD war veterans.

PubMed

Boričević Maršanić, Vlatka; Aukst Margetić, Branka; Jukić, Vlado; Matko, Vlasta; Grgić, Vesna

2014-05-01

The presence of posttraumatic stress disorder (PTSD) in male war veterans has been linked with family dysfunction and psychopathology in their children [1, 2]. This study aimed to evaluate self-reported emotional and behavioral symptoms, parent-adolescent bonding and family functioning in clinically referred adolescent offspring of Croatian PTSD war veterans and determine the degree that parent-child bonding and family functioning contributed to adolescent behavior problems. Internalizing and externalizing behavior problems, parent-child bonding and family functioning were assessed in a sample of clinically referred Croatian PTSD veterans adolescent offspring (N = 122) and non-PTSD veteran adolescent offspring (N = 122) matched for age, sex, educational level, family income, parental employment status, ethnicity, and residential area. Youth Self-Report, Parental Bonding Instrument, Family Assessment Device were used. Adolescent offspring of PTSD veterans reported having significantly more internalizing and externalizing problems than non-PTSD veteran offspring, and also more difficulties in their family functioning, lower levels of maternal and paternal care, and more impaired mother-child and father-child bonding than control subjects. Internalizing symptoms were associated with family dysfunction, while externalizing symptoms were associated with paternal overcontrol/overprotection, and low maternal and paternal care. In conclusion, the increase in internalizing and externalizing symptoms as well as family and parental dysfunction among clinically referred adolescent offspring of PTSD veterans compared to their non-PTSD veteran counterparts indicates a need for early detection and interventions targeting both adolescent psychopathology and family relationships.

Bond slip detection of concrete-encased composite structure using shear wave based active sensing approach

NASA Astrophysics Data System (ADS)

Zeng, Lei; Parvasi, Seyed Mohammad; Kong, Qingzhao; Huo, Linsheng; Lim, Ing; Li, Mo; Song, Gangbing

2015-12-01

Concrete-encased composite structure exhibits improved strength, ductility and fire resistance compared to traditional reinforced concrete, by incorporating the advantages of both steel and concrete materials. A major drawback of this type of structure is the bond slip introduced between steel and concrete, which directly reduces the load capacity of the structure. In this paper, an active sensing approach using shear waves to provide monitoring and early warning of the development of bond slip in the concrete-encased composite structure is proposed. A specimen of concrete-encased composite structure was investigated. In this active sensing approach, shear mode smart aggregates (SAs) embedded in the concrete act as actuators and generate desired shear stress waves. Distributed piezoceramic transducers installed in the cavities of steel plates act as sensors and detect the wave response from shear mode SAs. Bond slip acts as a form of stress relief and attenuates the wave propagation energy. Experimental results from the time domain analysis clearly indicate that the amplitudes of received signal by lead zirconate titanate sensors decreased when bond slip occurred. In addition, a wavelet packet-based analysis was developed to compute the received signal energy values, which can be used to determine the initiation and development of bond slip in concrete-encased composite structure. In order to establish the validity of the proposed method, a 3D finite element analysis of the concrete-steel bond model is further performed with the aid of the commercial finite element package, Abaqus, and the numerical results are compared with the results obtained in experimental study.

Metabolic modeling of dynamic brain 13C NMR multiplet data: Concepts and simulations with a two-compartment neuronal-glial model

PubMed Central

Shestov, Alexander A.; Valette, Julien; Deelchand, Dinesh K.; Uğurbil, Kâmil; Henry, Pierre-Gilles

2016-01-01

Metabolic modeling of dynamic 13C labeling curves during infusion of 13C-labeled substrates allows quantitative measurements of metabolic rates in vivo. However metabolic modeling studies performed in the brain to date have only modeled time courses of total isotopic enrichment at individual carbon positions (positional enrichments), not taking advantage of the additional dynamic 13C isotopomer information available from fine-structure multiplets in 13C spectra. Here we introduce a new 13C metabolic modeling approach using the concept of bonded cumulative isotopomers, or bonded cumomers. The direct relationship between bonded cumomers and 13C multiplets enables fitting of the dynamic multiplet data. The potential of this new approach is demonstrated using Monte-Carlo simulations with a brain two-compartment neuronal-glial model. The precision of positional and cumomer approaches are compared for two different metabolic models (with and without glutamine dilution) and for different infusion protocols ([1,6-13C2]glucose, [1,2-13C2]acetate, and double infusion [1,6-13C2]glucose + [1,2-13C2]acetate). In all cases, the bonded cumomer approach gives better precision than the positional approach. In addition, of the three different infusion protocols considered here, the double infusion protocol combined with dynamic bonded cumomer modeling appears the most robust for precise determination of all fluxes in the model. The concepts and simulations introduced in the present study set the foundation for taking full advantage of the available dynamic 13C multiplet data in metabolic modeling. PMID:22528840

Microwave emulations and tight-binding calculations of transport in polyacetylene

NASA Astrophysics Data System (ADS)

Stegmann, Thomas; Franco-Villafañe, John A.; Ortiz, Yenni P.; Kuhl, Ulrich; Mortessagne, Fabrice; Seligman, Thomas H.

2017-01-01

A novel approach to investigate the electron transport of cis- and trans-polyacetylene chains in the single-electron approximation is presented by using microwave emulation measurements and tight-binding calculations. In the emulation we take into account the different electronic couplings due to the double bonds leading to coupled dimer chains. The relative coupling constants are adjusted by DFT calculations. For sufficiently long chains a transport band gap is observed if the double bonds are present, whereas for identical couplings no band gap opens. The band gap can be observed also in relatively short chains, if additional edge atoms are absent, which cause strong resonance peaks within the band gap. The experimental results are in agreement with our tight-binding calculations using the nonequilibrium Green's function method. The tight-binding calculations show that it is crucial to include third nearest neighbor couplings to obtain the gap in the cis-polyacetylene.

Ab-initio study of structural, electronic, and transport properties of zigzag GaP nanotubes.

PubMed

Srivastava, Anurag; Jain, Sumit Kumar; Khare, Purnima Swarup

2014-03-01

Stability and electronic properties of zigzag (3 ≤ n ≤ 16) gallium phosphide nanotubes (GaP NTs) have been analyzed by employing a systematic ab-intio approach based on density functional theory using generalized gradient approximation with revised Perdew Burke Ernzerhoff type parameterization. Diameter dependence of bond length, buckling, binding energy, and band gap has been investigated and the analysis shows that the bond length and buckling decreases with increasing diameter of the tube, highest binding energy of (16, 0) confirms this as the most stable amongst all the NTs taken into consideration. The present GaP NTs shows direct band gap and it increases with diameter of the tubes. Using a two probe model for (4, 0) NT the I-V relationship shows an exponential increase in current on applying bias voltage beyond 1.73 volt.

Aggregation control of quantum dots through ion-mediated hydrogen bonding shielding.

PubMed

Liu, Jianbo; Yang, Xiaohai; Wang, Kemin; He, Xiaoxiao; Wang, Qing; Huang, Jin; Liu, Yan

2012-06-26

Nanoparticle stabilization against detrimental aggregation is a critical parameter that needs to be well controlled. Herein, we present a facile and rapid ion-mediated dispersing technique that leads to hydrophilic aggregate-free quantum dots (QDs). Because of the shielding of the hydrogen bonds between cysteamine-capped QDs, the presence of F(-) ions disassembled the aggregates of QDs and afforded their high colloidal stability. The F(-) ions also greatly eliminated the nonspecific adsorption of the QDs on glass slides and cells. Unlike the conventional colloidal stabilized method that requires the use of any organic ligand and/or polymer for the passivation of the nanoparticle surface, the proposed approach adopts the small size and large diffusion coefficient of inorganic ions as dispersant, which offers the disaggregation a fast reaction dynamics and negligible influence on their intrinsic surface functional properties. Therefore, the ion-mediated dispersing strategy showed great potential in chemosensing and biomedical applications.

Modular assembly of proteins on nanoparticles.

PubMed

Ma, Wenwei; Saccardo, Angela; Roccatano, Danilo; Aboagye-Mensah, Dorothy; Alkaseem, Mohammad; Jewkes, Matthew; Di Nezza, Francesca; Baron, Mark; Soloviev, Mikhail; Ferrari, Enrico

2018-04-16

Generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold-sulfur bonds (Au-S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.

Counteranion Driven Homochiral Assembly of a Cationic C3-Symmetric Gelator through Ion-Pair Assisted Hydrogen Bond.

PubMed

Maity, Arunava; Gangopadhyay, Monalisa; Basu, Arghya; Aute, Sunil; Babu, Sukumaran Santhosh; Das, Amitava

2016-09-07

The helical handedness in achiral self-assemblies is mostly complex due to spontaneous symmetry breaking or kinetically controlled random assembly formation. Here an attempt has been made to address this issue through chiral anion exchange. A new class of cationic achiral C3-symmetric gelator devoid of any conventional gelation assisting functional units is found to form both right- and left-handed helical structures. A chiral counteranion exchange-assisted approach is successfully introduced to control the chirality sign and thereby to obtain preferred homochiral assemblies. Formation of anion-assisted chiral assembly was confirmed by circular dichroism (CD) spectroscopy, microscopic images, and crystal structure. The X-ray crystal structure reveals the construction of helical assemblies with opposite handedness for (+)- and (-)-chiral anion reformed gelators. The appropriate counteranion driven ion-pair-assisted hydrogen-bonding interactions are found responsible for the helical bias control in this C3-symmetric gelator.

The structure of antimalarial dispiro-1,2,4-trioxolanes: A density functional approach

NASA Astrophysics Data System (ADS)

Moroni, L.; Salvi, P. R.

2006-02-01

Ab initio DF/B3-LYP/cc-pVDZ calculations have been performed on three dispiro-1,2,4-trioxolane systems ( 2)-( 4). Interest in these systems comes from the fact that a water-soluble derivative of ( 3), known as OZ277, has been synthesized and identified as antimalarial drug with activity superior to those of semisynthetic artemisinins. Structural data have been obtained regarding the atomic arrangement around the peroxide bond for the three systems. Making reference to ( 3), two conformers have been calculated depending on the axial or equatorial bond of spirocyclohexane with the peroxide oxygen of 1,2,4-trioxolane. In particular, while the peroxide oxygen on the spiroadamantane side is sterically hindered for both the axial and the equatorial conformer, the peroxide oxygen on the spirocyclohexane side is more accessible to external attack when the conformer is axial than when is equatorial.

Thermodynamic properties of small aggregates of rare-gas atoms

NASA Technical Reports Server (NTRS)

Etters, R. D.; Kaelberer, J.

1975-01-01

The present work reports on the equilibrium thermodynamic properties of small clusters of xenon, krypton, and argon atoms, determined from a biased random-walk Monte Carlo procedure. Cluster sizes ranged from 3 to 13 atoms. Each cluster was found to have an abrupt liquid-gas phase transition at a temperature much less than for the bulk material. An abrupt solid-liquid transition is observed for thirteen- and eleven-particle clusters. For cluster sizes smaller than 11, a gradual transition from solid to liquid occurred over a fairly broad range of temperatures. Distribution of number of bond lengths as a function of bond length was calculated for several systems at various temperatures. The effects of box boundary conditions are discussed. Results show the importance of a correct description of boundary conditions. A surprising result is the slow rate at which system properties approach bulk behavior as cluster size is increased.

Coupling of metals and biominerals: characterizing the interface between ferromagnetic shape-memory alloys and hydroxyapatite.

PubMed

Allenstein, Uta; Selle, Susanne; Tadsen, Meike; Patzig, Christian; Höche, Thomas; Zink, Mareike; Mayr, Stefan G

2015-07-22

Durable, mechanically robust osseointegration of metal implants poses one of the largest challenges in contemporary orthopedics. The application of biomimetic hydroxyapatite (HAp) coatings as mediators for enhanced mechanical coupling to natural bone constitutes a promising approach. Motivated by recent advances in the field of smart metals that might open the venue for alternate therapeutic concepts, we explore their mechanical coupling to sputter-deposited HAp layers in a combined experimental-theoretical study. While experimental delamination tests and comprehensive structural characterization, including high-resolution transmission electron microscopy, are utilized to establish structure-property relationships, density functional theory based total energy calculations unravel the underlying physics and chemistry of bonding and confirm the experimental findings. Experiments and modeling indicate that sputter-deposited HAp coatings are strongly adherent to the exemplary ferromagnetic shape-memory alloys, Ni-Mn-Ga and Fe-Pd, with delamination stresses and interface bonding strength exceeding the physiological scales by orders of magnitude.

Surface passivation for tight-binding calculations of covalent solids.

PubMed

Bernstein, N

2007-07-04

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp(3) hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Surface passivation for tight-binding calculations of covalent solids

NASA Astrophysics Data System (ADS)

Bernstein, N.

2007-07-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Molecular structure, vibrational spectroscopic (FT-IR, FT-Raman), UV-vis spectra, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis, thermodynamic properties of benzophenone 2,4-dicarboxylic acid by ab initio HF and density functional method

NASA Astrophysics Data System (ADS)

Chaitanya, K.

2012-02-01

The FT-IR (4000-450 cm -1) and FT-Raman spectra (3500-100 cm -1) of benzophenone 2,4-dicarboxylic acid (2,4-BDA) have been recorded in the condensed state. Density functional theory calculation with B3LYP/6-31G(d,p) basis set have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman activities and bonding features of the title compounds. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability ( β0) and related properties ( β, α0 and Δ α) of 2,4-BDA is calculated using HF/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charges is also calculated. Because of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-vis spectra and electronic absorption properties were explained and illustrated from the frontier molecular orbitals.

Readily functionalized AAA-DDD triply hydrogen-bonded motifs.

PubMed

Tong, Feng; Linares-Mendez, Iamnica J; Han, Yi-Fei; Wisner, James A; Wang, Hong-Bo

2018-04-25

Herein we present a new, readily functionalized AAA-DDD hydrogen bond array. A novel AAA monomeric unit (3a-b) was obtained from a two-step synthetic procedure starting with 2-aminonicotinaldehyde via microwave radiation (overall yield of 52-66%). 1H NMR and fluorescence spectroscopy confirmed the complexation event with a calculated association constant of 1.57 × 107 M-1. Likewise, the usefulness of this triple hydrogen bond motif in supramolecular polymerization was demonstrated through viscosity measurements in a crosslinked supramolecular alternating copolymer.

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.

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.

Multiconfiguration Pair-Density Functional Theory: A New Way To Treat Strongly Correlated Systems.

PubMed

Gagliardi, Laura; Truhlar, Donald G; Li Manni, Giovanni; Carlson, Rebecca K; Hoyer, Chad E; Bao, Junwei Lucas

2017-01-17

The electronic energy of a system provides the Born-Oppenheimer potential energy for internuclear motion and thus determines molecular structure and spectra, bond energies, conformational energies, reaction barrier heights, and vibrational frequencies. The development of more efficient and more accurate ways to calculate the electronic energy of systems with inherently multiconfigurational electronic structure is essential for many applications, including transition metal and actinide chemistry, systems with partially broken bonds, many transition states, and most electronically excited states. Inherently multiconfigurational systems are called strongly correlated systems or multireference systems, where the latter name refers to the need for using more than one ("multiple") configuration state function to provide a good zero-order reference wave function. This Account describes multiconfiguration pair-density functional theory (MC-PDFT), which was developed as a way to combine the advantages of wave function theory (WFT) and density functional theory (DFT) to provide a better treatment of strongly correlated systems. First we review background material: the widely used Kohn-Sham DFT (which uses only a single Slater determinant as reference wave function), multiconfiguration WFT methods that treat inherently multiconfigurational systems based on an active space, and previous attempts to combine multiconfiguration WFT with DFT. Then we review the formulation of MC-PDFT. It is a generalization of Kohn-Sham DFT in that the electron kinetic energy and classical electrostatic energy are calculated from a reference wave function, while the rest of the energy is obtained from a density functional. However, there are two main differences with respent to Kohn-Sham DFT: (i) The reference wave function is multiconfigurational rather than being a single Slater determinant. (ii) The density functional is a function of the total density and the on-top pair density rather than being a function of the spin-up and spin-down densities. In work carried out so far, the multiconfigurational wave function is a multiconfiguration self-consistent-field wave function. The new formulation has the advantage that the reference wave function has the correct spatial and spin symmetry and can describe bond dissociation (of both single and multiple bonds) and electronic excitations in a formally and physically correct way. We then review the formulation of density functionals in terms of the on-top pair density. Finally we review successful applications of the theory to bond energies and bond dissociation potential energy curves of main-group and transition metal bonds, to barrier heights (including pericyclic reactions), to proton affinities, to the hydrogen bond energy of water dimer, to ground- and excited-state charge transfer, to valence and Rydberg excitations of molecules, and to singlet-triplet splittings of radicals. We find that that MC-PDFT can give accurate results not only with complete-active-space multiconfiguration wave functions but also with generalized-active-space multiconfiguration wave functions, which are practical for larger numbers of active electrons and active orbitals than are complete-active-space wave functions. The separated-pair approximation, which is a special case of generalized active space self-consistent-field theory, is especially promising. MC-PDFT, because it requires much less computer time and storage than pure WFT methods, has the potential to open larger and more complex strongly correlated systems to accurate simulation.

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.

High-temperature adhesives for bonding polyimide film. [bonding Kapton film for solar sails

NASA Technical Reports Server (NTRS)

St.clair, A. K.; Slemp, W. S.; St.clair, T. L.

1980-01-01

Experimental polyimide resins were developed and evaluated as potential high temperature adhesives for bonding Kapton polyimide film. Lap shear strengths of Kapton/Kapton bonds were obtained as a function of test temperature, adherend thickness, and long term aging at 575 K (575 F) in vacuum. Glass transition temperatures of the polyimide/"Kapton" bondlines were monitored by thermomechanical analysis.

Alkyl Aryl Ether Bond Formation with PhenoFluor**

PubMed Central

Shen, Xiao; Neumann, Constanze N.; Kleinlein, Claudia; Claudia, Nathaniel W.; Ritter, Tobias

2015-01-01

An alkyl aryl ether bond formation reaction between phenols and primary and secondary alcohols with PhenoFluor has been developed. The reaction features a broad substrate scope and tolerates many functional groups, and substrates that are challenging for more conventional ether bond forming processes may be coupled. A preliminary mechanistic study indicates reactivity distinct from conventional ether bond formation. PMID:25800679

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.

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.

Quantum Chemical Studies of Actinides and Lanthanides: From Small Molecules to Nanoclusters

NASA Astrophysics Data System (ADS)

Vlaisavljevich, Bess

Research into actinides is of high interest because of their potential applications as an energy source and for the environmental implications therein. Global concern has arisen since the development of the actinide concept in the 1940s led to the industrial scale use of the commercial nuclear energy cycle and nuclear weapons production. Large quantities of waste have been generated from these processes inspiring efforts to address fundamental questions in actinide science. In this regard, the objective of this work is to use theory to provide insight and predictions into actinide chemistry, where experimental work is extremely challenging because of the intrinsic difficulties of the experiments themselves and the safety issues associated with this type of chemistry. This thesis is a collection of theoretical studies of actinide chemistry falling into three categories: quantum chemical and matrix isolation studies of small molecules, the electronic structure of organoactinide systems, and uranyl peroxide nanoclusters and other solid state actinide compounds. The work herein not only spans a wide range of systems size but also investigates a range of chemical problems. Various quantum chemical approaches have been employed. Wave function-based methods have been used to study the electronic structure of actinide containing molecules of small to middle-size. Among these methods, the complete active space self consistent field (CASSCF) approach with corrections from second-order perturbation theory (CASPT2), the generalized active space SCF (GASSCF) approach, and Moller-Plesset second-order perturbation theory (MP2) have been employed. Likewise, density functional theory (DFT) has been used along with analysis tools like bond energy decomposition, bond orders, and Bader's Atoms in Molecules. From these quantum chemical results, comparison with experimentally obtained structures and spectra are made.

A periodic energy decomposition analysis method for the investigation of chemical bonding in extended systems

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

Raupach, Marc; Tonner, Ralf, E-mail: tonner@chemie.uni-marburg.de

The development and first applications of a new periodic energy decomposition analysis (pEDA) scheme for extended systems based on the Kohn-Sham approach to density functional theory are described. The pEDA decomposes the bonding energy between two fragments (e.g., the adsorption energy of a molecule on a surface) into several well-defined terms: preparation, electrostatic, Pauli repulsion, and orbital relaxation energies. This is complemented by consideration of dispersion interactions via a pairwise scheme. One major extension toward a previous implementation [Philipsen and Baerends, J. Phys. Chem. B 110, 12470 (2006)] lies in the separate discussion of electrostatic and Pauli and the additionmore » of a dispersion term. The pEDA presented here for an implementation based on atomic orbitals can handle restricted and unrestricted fragments for 0D to 3D systems considering periodic boundary conditions with and without the determination of fragment occupations. For the latter case, reciprocal space sampling is enabled. The new method gives comparable results to established schemes for molecular systems and shows good convergence with respect to the basis set (TZ2P), the integration accuracy, and k-space sampling. Four typical bonding scenarios for surface-adsorbate complexes were chosen to highlight the performance of the method representing insulating (CO on MgO(001)), metallic (H{sub 2} on M(001), M = Pd, Cu), and semiconducting (CO and C{sub 2}H{sub 2} on Si(001)) substrates. These examples cover diverse substrates as well as bonding scenarios ranging from weakly interacting to covalent (shared electron and donor acceptor) bonding. The results presented lend confidence that the pEDA will be a powerful tool for the analysis of surface-adsorbate bonding in the future, enabling the transfer of concepts like ionic and covalent bonding, donor-acceptor interaction, steric repulsion, and others to extended systems.« less

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.

Methods For Self-Organizing Software

DOEpatents

Bouchard, Ann M.; Osbourn, Gordon C.

2005-10-18

A method for dynamically self-assembling and executing software is provided, containing machines that self-assemble execution sequences and data structures. In addition to ordered functions calls (found commonly in other software methods), mutual selective bonding between bonding sites of machines actuates one or more of the bonding machines. Two or more machines can be virtually isolated by a construct, called an encapsulant, containing a population of machines and potentially other encapsulants that can only bond with each other. A hierarchical software structure can be created using nested encapsulants. Multi-threading is implemented by populations of machines in different encapsulants that are interacting concurrently. Machines and encapsulants can move in and out of other encapsulants, thereby changing the functionality. Bonding between machines' sites can be deterministic or stochastic with bonding triggering a sequence of actions that can be implemented by each machine. A self-assembled execution sequence occurs as a sequence of stochastic binding between machines followed by their deterministic actuation. It is the sequence of bonding of machines that determines the execution sequence, so that the sequence of instructions need not be contiguous in memory.

Toward the Prediction of Water Exchange Rates in Magnetic Resonance Imaging Contrast Agents: A Density Functional Theory Study.

PubMed

Regueiro-Figueroa, Martín; Platas-Iglesias, Carlos

2015-06-18

We present a theoretical investigation of Gd-Owater bonds in different complexes relevant as contrast agents in magnetic resonance imaging (MRI). The analysis of the Ln-Owater distances, electron density (ρBCP), and electron localization function (ELF) at the bond critical points of [Ln(DOTA)(H2O)](-) and [Ln(DTPA-BMA)(H2O)] indicates that the strength of the Ln-Owater bonds follows the order DTPA-BMA > DOTA (M isomer) > DOTA (m isomer). The ELF values decrease along the 4f period as the Ln-Owater bonds get shorter, in line with the labile capping bond phenomenon. Extension of these calculations to other Gd(3+) complexes allowed us to correlate the experimentally observed water exchange rates and the calculated ρBCP and ELF values. The water exchange reaction becomes faster as the Gd-Owater bonds are weakened, which is reflected in longer bond distances and lower values of ρBCP and ELF. DKH2 calculations show that the two coordinated water molecules may also have significantly different (17)O hyperfine coupling constants (HFCCs).

Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis.

PubMed

Park, In-Hee; Venable, John D; Steckler, Caitlin; Cellitti, Susan E; Lesley, Scott A; Spraggon, Glen; Brock, Ansgar

2015-09-28

Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure, and dynamics. More recently, hydrogen exchange mass spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from molecular dynamics (MD) simulation snapshots is used to determine partitioning over bonded and nonbonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of residue resolved protection factor predictions for staphylococcal nuclease with NMR data, which was also used to compare prediction performance with other algorithms described in the literature. The demonstrated transferable and scalable MD based HX prediction approach adds significantly to the available tools for HX-MS data interpretation based on available structures and models.

Pattern similarity study of functional sites in protein sequences: lysozymes and cystatins

PubMed Central

Nakai, Shuryo; Li-Chan, Eunice CY; Dou, Jinglie

2005-01-01

Background Although it is generally agreed that topography is more conserved than sequences, proteins sharing the same fold can have different functions, while there are protein families with low sequence similarity. An alternative method for profile analysis of characteristic conserved positions of the motifs within the 3D structures may be needed for functional annotation of protein sequences. Using the approach of quantitative structure-activity relationships (QSAR), we have proposed a new algorithm for postulating functional mechanisms on the basis of pattern similarity and average of property values of side-chains in segments within sequences. This approach was used to search for functional sites of proteins belonging to the lysozyme and cystatin families. Results Hydrophobicity and β-turn propensity of reference segments with 3–7 residues were used for the homology similarity search (HSS) for active sites. Hydrogen bonding was used as the side-chain property for searching the binding sites of lysozymes. The profiles of similarity constants and average values of these parameters as functions of their positions in the sequences could identify both active and substrate binding sites of the lysozyme of Streptomyces coelicolor, which has been reported as a new fold enzyme (Cellosyl). The same approach was successfully applied to cystatins, especially for postulating the mechanisms of amyloidosis of human cystatin C as well as human lysozyme. Conclusion Pattern similarity and average index values of structure-related properties of side chains in short segments of three residues or longer were, for the first time, successfully applied for predicting functional sites in sequences. This new approach may be applicable to studying functional sites in un-annotated proteins, for which complete 3D structures are not yet available. PMID:15904486

A periodic mixed gaussians-plane waves DFT study on simple thiols on Au(111): adsorbate species, surface reconstruction, and thiols functionalization.

PubMed

Rajaraman, Gopalan; Caneschi, Andrea; Gatteschi, Dante; Totti, Federico

2011-03-07

Here we present DFT calculations based on a periodic mixed gaussians/plane waves approach to study the energetics, structure, bonding of SAMs of simple thiols on Au(111). Several open issues such as structure, bonding and the nature of adsorbate are taken into account. We started with methyl thiols (MeSH) on Au(111) to establish the nature of the adsorbate. We have considered several structural models embracing the reconstructed surface scenario along with the MeS˙-Au(ad)-MeS˙ type motif put forward in recent years. Our calculations suggest a clear preference for the homolytic cleavage of the S-H bond leading to a stable MeS˙ on a gold surface. In agreement with the recent literature studies, the reconstructed models of the MeS˙ species are found to be energetically preferred over unreconstructed models. Besides, our calculations reveal that the model with 1:2 Au(ad)/thiols ratio, i.e. MeS˙-Au(ad)-MeS˙, is energetically preferred compared to the clean and 1:1 ratio models, in agreement with the experimental and theoretical evidences. We have also performed Molecular Orbital/Natural Bond Orbital, MO/NBO, analysis to understand the electronic structure and bonding in different structural motifs and many useful insights have been gained. Finally, the studies have then been extended to alkyl thiols of the RSR' (R, R' = Me, Et and Ph) type and here our calculations again reveal a preference for the RS˙ type species adsorption for clean as well as for reconstructed 1:2 Au(ad)/thiols ratio models.

Micro-oxidation treatment to improve bonding strength of Sr and Na co-substituted hydroxyapatite coatings for carbon/carbon composites

NASA Astrophysics Data System (ADS)

Zhang, Leilei; Li, Hejun; Li, Kezhi; Zhang, Yulei; Liu, Shoujie; Guo, Qian; Li, Shaoxian

2016-08-01

To improve the bonding strength of Sr and Na co-substituted hydroxyapatite (SNH) coatings for carbon/carbon composites, carbon/carbon composites are surface modified by micro-oxidation treatment. The micro-oxidation treatment could generate large number of pores containing oxygenic functional groups on the surface of carbon/carbon composites. SNH is nucleated on the inwall of the pores and form a flaky shape coating with 10-50 nm in thickness and 200-900 nm in width. The bonding strength between SNH coating and carbon/carbon composites increases from 4.27 ± 0.26 MPa to 10.57 ± 0.38 MPa after the micro-oxidation treatment. The promotion of bonding strength is mainly attributed to the pinning effect caused by the pores and chemical bonding generated by the oxygenic functional groups.

Pricing index-based catastrophe bonds: Part 1: Formulation and discretization issues using a numerical PDE approach

NASA Astrophysics Data System (ADS)

Unger, André J. A.

2010-02-01

This work is the first installment in a two-part series, and focuses on the development of a numerical PDE approach to price components of a Bermudan-style callable catastrophe (CAT) bond. The bond is based on two underlying stochastic variables; the PCS index which posts quarterly estimates of industry-wide hurricane losses as well as a single-factor CIR interest rate model for the three-month LIBOR. The aggregate PCS index is analogous to losses claimed under traditional reinsurance in that it is used to specify a reinsurance layer. The proposed CAT bond model contains a Bermudan-style call feature designed to allow the reinsurer to minimize their interest rate risk exposure on making substantial fixed coupon payments using capital from the reinsurance premium. Numerical PDE methods are the fundamental strategy for pricing early-exercise constraints, such as the Bermudan-style call feature, into contingent claim models. Therefore, the objective and unique contribution of this first installment in the two-part series is to develop a formulation and discretization strategy for the proposed CAT bond model utilizing a numerical PDE approach. Object-oriented code design is fundamental to the numerical methods used to aggregate the PCS index, and implement the call feature. Therefore, object-oriented design issues that relate specifically to the development of a numerical PDE approach for the component of the proposed CAT bond model that depends on the PCS index and LIBOR are described here. Formulation, numerical methods and code design issues that relate to aggregating the PCS index and introducing the call option are the subject of the companion paper.

Sol-gel approach for fabrication of coated anodized titanium wire for solid-phase microextraction: highly efficient adsorbents for enrichment of trace polar analytes.

PubMed

Jia, Jing; Xu, Lili; Wang, Shuai; Wang, Licheng; Liu, Xia

2014-05-01

Nanotubular titania film was prepared in situ on titanium wire and was used as the fiber substrate for solid-phase microextraction (SPME) because of its high surface-to-volume ratio, easy preparation, and mechanical stability. Three different functional coatings, β-cyclodextrin (β-CD), β-cyclodextrin-co-poly(ethylenepropylene glycol) (β-CD/PEG), and polyethylene glycol (PEG)-based sorbents were chemically bonded to the nanostructured wire surface via sol-gel technology to further enhance the absorbing capability and extraction selectivity. Coupled to gas chromatography-flame ionic detection (GC-FID), the prepared SPME fibers were investigated using diverse compounds. The results indicated that the fibers showed good mechanical strength, excellent thermal stability, and wonderful capacity and selectivity to polar compounds, including polar aromatic compounds, alcohols, and ketones. Combining the superior hydrophilic property of a bonded functional molecule and the highly porous structure of a fiber coating, the prepared PEG-coated SPME fiber showed much higher adsorption affinity to ephedrine and methylephedrine than β-CD and β-CD/PEG fibers. The as-established PEG-coated SPME-GC analytical method provided excellent sensitivity (LODs, 0.004 and 0.001 ng mL(-1) for ephedrine and methylephedrine, respectively) and better linear range (0.01-2 000 μg L(-1)). In addition, it has surprising repeatability and reproducibility. Finally, the present approach was used to analyze ephedrine and methylephedrine from real urine samples, and reliable results were obtained.

Mechanical Attachment of Reusable Surface Insulation to Space Shuttle Primary Structure

NASA Technical Reports Server (NTRS)

Fleck, R. W.; Lehman, J. K.

1973-01-01

Three methods of attaching surface insulation tiles to shuttle primary structure have been proposed: direct bond, mechanical attachment, and subpanels with standoffs. The direct bond approach is lightweight but is difficult to refurbish and inspect. The subpanel approach is heavier but allows for easy refurbishment since subpanels are easily removed and replaced. The mechanical attachment approach allows easy refurbishment and inspection and is lightweight when an efficient insulator is used between surface insulation tiles and primary structure.

Cyclo-biphenalenyl biradicaloid molecular materials: conformation, rearrangement, magnetism, and thermochromism

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

Huang, Jingsong; Sumpter, Bobby G; Meunier, Vincent

2010-01-01

Cyclo-biphenalenyl biradicaloid molecular materials with chair- and boat-conformations are studied by restricted and broken-symmetry DFT using the M06 family of meta-GGA functionals. The global minima of these molecular materials are magnetically silent due to the sigma-bond connecting the two phenalenyls, while the sigma-bond may undergo low-barrier sigmatropic rearrangements via pi-pi bonded paramagnetic intermediates. The validation of theory is performed for the chair-conformation by comparing the sigma-bonded structures and the rearrangement barriers with experimental data. The boat-conformation is then studied using the validated functional. The electronic spectra of both chair- and boat-conformations are calculated and their applications in thermochromism are discussed.

Bond Order and Chemical Properties of BF, CO, and N[subscript 2

ERIC Educational Resources Information Center

Martinie, Ryan J.; Bultema, Jarred J.; Vander Wal, Mark N.; Burkhart, Brandon J.; Vander Griend, Douglas A.; DeKock, Roger L.

2011-01-01

The traditional chemical approaches, Lewis electron dot structures and molecular orbital theory, predict the relative bond orders of boron monofluoride, carbon monoxide, and dinitrogen to be BF less than CO less than N[subscript 2]. This is quantified by quantum mechanical, theoretical studies that show the bond orders to be approximately 1.4,…

De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity

PubMed Central

Boyken, Scott E.; Chen, Zibo; Groves, Benjamin; Langan, Robert A.; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H.; Baker, David

2017-01-01

In nature, structural specificity in DNA and proteins is encoded quite differently: in DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen bond networks with atomic accuracy is a milestone for protein design and enables the programming of protein interaction specificity for a broad range of synthetic biology applications. PMID:27151862

Silicone-containing composition

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

Mohamed, Mustafa

A silicone-containing composition comprises the reaction product of a first component and an excess of an isocyanate component relative to the first component to form an isocyanated intermediary. The first component is selected from one of a polysiloxane and a silicone resin. The first component includes a carbon-bonded functional group selected from one of a hydroxyl group and an amine group. The isocyanate component is reactive with the carbon-bonded functional group of the first component. The isocyanated intermediary includes a plurality of isocyanate functional groups. The silicone-containing composition comprises the further reaction product of a second component, which is selectedmore » from the other of the polysiloxane and the silicone resin. The second component includes a plurality of carbon-bonded functional groups reactive with the isocyanate functional groups of the isocyanated intermediary for preparing the silicone-containing composition.« less

AIEgens-Functionalized Inorganic-Organic Hybrid Materials: Fabrications and Applications.

PubMed

Li, Dongdong; Yu, Jihong

2016-12-01

Inorganic materials functionalized with organic fluorescent molecules combine advantages of them both, showing potential applications in biomedicine, chemosensors, light-emitting, and so on. However, when more traditional organic dyes are doped into the inorganic materials, the emission of resulting hybrid materials may be quenched, which is not conducive to the efficiency and sensitivity of detection. In contrast to the aggregation-caused quenching (ACQ) system, the aggregation-induced emission luminogens (AIEgens) with high solid quantum efficiency, offer new potential for developing highly efficient inorganic-organic hybrid luminescent materials. So far, many AIEgens have been incorporated into inorganic materials through either physical doping caused by aggregation induced emission (AIE) or chemical bonding (e.g., covalent bonding, ionic bonding, and coordination bonding) caused by bonding induced emission (BIE) strategy. The hybrid materials exhibit excellent photoactive properties due to the intramolecular motion of AIEgens is restricted by inorganic matrix. Recent advances in the fabrication of AIEgens-functionalized inorganic-organic hybrid materials and their applications in biomedicine, chemical sensing, and solid-state light emitting are presented. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional biomimetic analogs help remineralize apatite-depleted demineralized resin-infiltrated dentin via a bottom-up approach

PubMed Central

Kim, Jongryul; Arola, Dwayne D.; Gu, Lisha; Kim, Young Kyung; Mai, Sui; Liu, Yan; Pashley, David H.; Tay, Franklin R.

2010-01-01

Natural biominerals are formed through metastable amorphous precursor phases via a bottom-up, nanoparticle-mediated mineralization mechanism. Using an acid-etched human dentin model to create a layer of completely-demineralized collagen matrix, a bio-inspired mineralization scheme has been developed based on the use of dual biomimetic analogs. These analogs help to sequester fluidic amorphous calcium phosphate nanoprecursors and function as templates for guiding homogeneous apatite nucleation within the collagen fibrils. By adopting this scheme for remineralizing adhesive resin-bonded, completely-demineralized dentin, we have been able to redeposit intrafibrillar and extrafibrillar apatites in completely-demineralized collagen matrices that are imperfectly infiltrated by resins. This study utilizes a spectrum of completely- and partially-demineralized dentin collagen matrices to further validate the necessity for using a biomimetic analog-containing medium for remineralizing resin-infiltrated partially-demineralized collagen matrices in which remnant seed crystallites are present. In control specimens in which biomimetic analogs are absent from the remineralization medium, remineralization could only be seen in partially-demineralized collagen matrices probably by epitaxial growth via a top-down crystallization approach. Conversely, in the presence of biomimetic analogs in the remineralization medium, intrafibrillar remineralization of completely-demineralized collagen matrices via a bottom-up crystallization mechanism can additionally be identified. The latter is characterized by the transition of intrafibrillar minerals from an inchoate state of continuously-braided microfibrillar electron-dense amorphous strands to discrete nanocrystals, and ultimately into larger crystalline platelets within the collagen fibrils. Biomimetic remineralization via dual biomimetic analogs has the potential to be translated into a functional delivery system for salvaging failing resin-dentin bonds. PMID:20045745

Functional biomimetic analogs help remineralize apatite-depleted demineralized resin-infiltrated dentin via a bottom-up approach.

PubMed

Kim, Jongryul; Arola, Dwayne D; Gu, Lisha; Kim, Young Kyung; Mai, Sui; Liu, Yan; Pashley, David H; Tay, Franklin R

2010-07-01

Natural biominerals are formed through metastable amorphous precursor phases via a bottom-up, nanoparticle-mediated mineralization mechanism. Using an acid-etched human dentin model to create a layer of completely demineralized collagen matrix, a bio-inspired mineralization scheme has been developed based on the use of dual biomimetic analogs. These analogs help to sequester fluidic amorphous calcium phosphate nanoprecursors and function as templates for guiding homogeneous apatite nucleation within the collagen fibrils. By adopting this scheme for remineralizing adhesive resin-bonded, completely demineralized dentin, we have been able to redeposit intrafibrillar and extrafibrillar apatites in completely demineralized collagen matrices that are imperfectly infiltrated by resins. This study utilizes a spectrum of completely and partially demineralized dentin collagen matrices to further validate the necessity for using a biomimetic analog-containing medium for remineralizing resin-infiltrated partially demineralized collagen matrices in which remnant seed crystallites are present. In control specimens in which biomimetic analogs are absent from the remineralization medium, remineralization could only be seen in partially demineralized collagen matrices, probably by epitaxial growth via a top-down crystallization approach. Conversely, in the presence of biomimetic analogs in the remineralization medium, intrafibrillar remineralization of completely demineralized collagen matrices via a bottom-up crystallization mechanism can additionally be identified. The latter is characterized by the transition of intrafibrillar minerals from an inchoate state of continuously braided microfibrillar electron-dense amorphous strands to discrete nanocrystals, and ultimately into larger crystalline platelets within the collagen fibrils. Biomimetic remineralization via dual biomimetic analogs has the potential to be translated into a functional delivery system for salvaging failing resin-dentin bonds. Copyright 2009 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Electronic structure investigations of 4-aminophthal hydrazide by UV-visible, NMR spectral studies and HOMO-LUMO analysis by ab initio and DFT calculations.

PubMed

Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M

2015-08-05

Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. Copyright © 2015 Elsevier B.V. All rights reserved.

Density function theoretical study on the complex involved in Th atom-activated C-C bond in C2H6

NASA Astrophysics Data System (ADS)

Qing-Qing, Wang; Peng, Li; Tao, Gao; Hong-Yan, Wang; Bing-Yun, Ao

2016-06-01

Density functional theory (DFT) calculations are performed to investigate the reactivity of Th atom toward ethane C-C bond activation. A comprehensive description of the reaction mechanisms leading to two different reaction products is presented. We report a complete exploration of the potential energy surfaces by taking into consideration different spin states. In addition, the intermediate and transition states along the reaction paths are characterized. Total, partial, and overlap population density of state diagrams and analyses are also presented. Furthermore, the natures of the chemical bonding of intermediate and transition states are studied by using topological method combined with electron localization function (ELF) and Mayer bond order. Infrared spectrum (IR) is obtained and further discussed based on the optimized geometries. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160, 21401173, and 11364023).

Ir-Catalyzed, Silyl-Directed, peri-Borylation of C-H Bonds in Fused Polycyclic Arenes and Heteroarenes.

PubMed

Su, Bo; Hartwig, John F

2018-05-20

peri-Disubstituted naphthalenes exhibit interesting physical properties and unique chemical reactivity, due to the parallel arrangement of the bonds to the two peri-disposed substituents. Regioselective installation of a functional group at the position peri to 1-substituted naphthalenes is challenging due to the steric interaction between the existing substituent and the position at which the second one would be installed. We report an iridium-catalyzed borylation of the C-H bond peri to a silyl group in naphthalenes and analogous polyaromatic hydrocarbons. The reaction occurs under mild conditions with wide functional group tolerance. The silyl group and the boryl group in the resulting products are precursors to a range of functional groups bound to the naphthalene ring through C-C, C-O, C-N, C-Br and C-Cl bonds. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

G3//BMK and Its Application to Calculation of Bond Dissociation Enthalpies.

PubMed

Zheng, Wen-Rui; Fu, Yao; Guo, Qing-Xiang

2008-08-01

On the basis of systematic examinations it was found that the BMK functional significantly outperformed the other popular density functional theory methods including B3LYP, B3P86, KMLYP, MPW1P86, O3LYP, and X3LYP for the calculation of bond dissociation enthalpies (BDEs). However, it was also found that even the BMK functional might dramatically fail in predicting the BDEs of some chemical bonds. To solve this problem, a new composite ab initio method named G3//BMK was developed by combining the strengths of both the G3 theory and BMK. G3//BMK was found to outperform the G3 and G3//B3LYP methods. It could accurately predict the BDEs of diverse types of chemical bonds in various organic molecules within a precision of ca. 1.2 kcal/mol.

26 CFR 1.150-1 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... material to the plan of financing include the purposes for the bonds and the structure of the financing..., structures involving windows or unreasonable allocations of bonds). (3) Exception for certain bonds financing... functionally related capital projects, and financing any clearly discrete governmental purpose). Each of these...

26 CFR 1.150-1 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... material to the plan of financing include the purposes for the bonds and the structure of the financing..., structures involving windows or unreasonable allocations of bonds). (3) Exception for certain bonds financing... functionally related capital projects, and financing any clearly discrete governmental purpose). Each of these...

HYDROGEN BONDING IN THE METHANOL DIMER

USDA-ARS?s Scientific Manuscript database

In this work, two methanol molecules are placed in different arrangements to study hydrogen bonding in carbohydrate materials such as cellulose. Energy was calculated as a function of both hydrogen bond length and angle over wide ranges, using quantum mechanics (QM). The QM wavefunctions are analyze...

Stability and electronic structure of the low- Σ grain boundaries in CdTe: a density functional study

DOE PAGES

Park, Ji-Sang; Kang, Joongoo; Yang, Ji-Hui; ...

2015-01-15

Using first-principles density functional calculations, we investigate the relative stability and electronic structure of the grain boundaries (GBs) in zinc-blende CdTe. Among the low-Σ-value symmetric tilt Σ3 (111), Σ3 (112), Σ5 (120), and Σ5 (130) GBs, we show that the Σ3 (111)GB is always the most stable due to the absence of dangling bonds and wrong bonds. The Σ5 (120) GBs, however, are shown to be more stable than the Σ3 (112) GBs, even though the former has a higher Σ value, and the latter is often used as a model system to study GB effects in zinc-blende semiconductors. Furthermore,more » we find that although containing wrong bonds, the Σ5 (120) GBs are electrically benign due to the short wrong bond lengths, and thus are not as harmful as the Σ3 (112) GBs also having wrong bonds but with longer bond lengths.« less

Highly efficient perturbative + variational strategy based on orthogonal valence bond theory for the evaluation of magnetic coupling constants. Application to the trinuclear Cu(ii) site of multicopper oxidases.

PubMed

Tenti, Lorenzo; Maynau, Daniel; Angeli, Celestino; Calzado, Carmen J

2016-07-21

A new strategy based on orthogonal valence-bond analysis of the wave function combined with intermediate Hamiltonian theory has been applied to the evaluation of the magnetic coupling constants in two AF systems. This approach provides both a quantitative estimate of the J value and a detailed analysis of the main physical mechanisms controlling the coupling, using a combined perturbative + variational scheme. The procedure requires a selection of the dominant excitations to be treated variationally. Two methods have been employed: a brute-force selection, using a logic similar to that of the CIPSI approach, or entanglement measures, which identify the most interacting orbitals in the system. Once a reduced set of excitations (about 300 determinants) is established, the interaction matrix is dressed at the second-order of perturbation by the remaining excitations of the CI space. The diagonalization of the dressed matrix provides J values in good agreement with experimental ones, at a very low-cost. This approach demonstrates the key role of d → d* excitations in the quantitative description of the magnetic coupling, as well as the importance of using an extended active space, including the bridging ligand orbitals, for the binuclear model of the intermediates of multicopper oxidases. The method is a promising tool for dealing with complex systems containing several active centers, as an alternative to both pure variational and DFT approaches.

Overview on the Surface Functionalization Mechanism and Determination of Surface Functional Groups of Plasma Treated Carbon Nanotubes.

PubMed

Saka, Cafer

2018-01-02

The use of carbon materials for many applications is due to the unique diversity of structures and properties ranging from chemical bonds between the carbon atoms of the materials to nanostructures, crystallite alignment, and microstructures. Carbon nanotubes and other nanoscale carbonaceous materials draw much attention due to their physical and chemical properties, such as high strength, high resistance to corrosion, electrical and thermal conductivity, stability and a qualified adsorbent. Carbon-based nanomaterials, which have a relatively large specific area and layered structure, can be used as an adsorbent for efficient removal of organic and inorganic contaminants. However, one of the biggest obstacles to the development of carbon-based nanomaterials adsorbents is insolubility and the lack of functional groups on the surface. There are several approaches to introduce functional groups on carbon nanotubes. One of these approaches, plasma applications, now has an important place in the creation of surface functional groups as a flexible, fast, and environmentally friendly method. This review focuses on recent information concerning the surface functionalization and modification of plasma treated carbon nanotube. This review considers the surface properties, advantages, and disadvantages of plasma-applied carbon nanotubes. It also examines the reaction mechanisms involved in the functional groups on the surface.

Atomic resolution chemical bond analysis of oxygen in La2CuO4

NASA Astrophysics Data System (ADS)

Haruta, M.; Nagai, T.; Lugg, N. R.; Neish, M. J.; Nagao, M.; Kurashima, K.; Allen, L. J.; Mizoguchi, T.; Kimoto, K.

2013-08-01

The distorted CuO6 octahedron in La2CuO4 was studied using aberration-corrected scanning transmission electron microscopy at atomic resolution. The near-edge structure in the oxygen K-edge electron energy-loss spectrum was recorded as a function of the position of the electron probe. After background subtraction, the measured spectrum image was processed using a recently developed inversion process to remove the mixing of signals on the atomic columns due to elastic and thermal scattering. The spectra were then compared with first-principles band structure calculations based on the local-density approximation plus on-site Coulomb repulsion (LDA + U) approach. In this article, we describe in detail not only anisotropic chemical bonding of the oxygen 2p state with the Cu 3d state but also with the Cu 4p and La 5d/4f states. Furthermore, it was found that buckling of the CuO2 plane was also detectable at the atomic resolution oxygen K-edge. Lastly, it was found that the effects of core-hole in the O K-edge were strongly dependent on the nature of the local chemical bonding, in particular, whether it is ionic or covalent.

Nonlinear Analysis of Bonded Composite Tubular Lap Joints

NASA Technical Reports Server (NTRS)

Oterkus, E.; Madenci, E.; Smeltzer, S. S., III; Ambur, D. R.

2005-01-01

The present study describes a semi-analytical solution method for predicting the geometrically nonlinear response of a bonded composite tubular single-lap joint subjected to general loading conditions. The transverse shear and normal stresses in the adhesive as well as membrane stress resultants and bending moments in the adherends are determined using this method. The method utilizes the principle of virtual work in conjunction with nonlinear thin-shell theory to model the adherends and a cylindrical shear lag model to represent the kinematics of the thin adhesive layer between the adherends. The kinematic boundary conditions are imposed by employing the Lagrange multiplier method. In the solution procedure, the displacement components for the tubular joint are approximated in terms of non-periodic and periodic B-Spline functions in the longitudinal and circumferential directions, respectively. The approach presented herein represents a rapid-solution alternative to the finite element method. The solution method was validated by comparison against a previously considered tubular single-lap joint. The steep variation of both peeling and shearing stresses near the adhesive edges was successfully captured. The applicability of the present method was also demonstrated by considering tubular bonded lap-joints subjected to pure bending and torsion.

Dynamic structural disorder in supported nanoscale catalysts

NASA Astrophysics Data System (ADS)

Rehr, J. J.; Vila, F. D.

2014-04-01

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

Computation of deuterium isotope perturbation of 13C NMR chemical shifts of alkanes: a local mode zero-point level approach.

PubMed

Yang, Kin S; Hudson, Bruce

2010-11-25

Replacement of H by D perturbs the (13)C NMR chemical shifts of an alkane molecule. This effect is largest for the carbon to which the D is attached, diminishing rapidly with intervening bonds. The effect is sensitive to stereochemistry and is large enough to be measured reliably. A simple model based on the ground (zero point) vibrational level and treating only the C-H(D) degrees of freedom (local mode approach) is presented. The change in CH bond length with H/D substitution as well as the reduction in the range of the zero-point level probability distribution for the stretch and both bend degrees of freedom are computed. The (13)C NMR chemical shifts are computed with variation in these three degrees of freedom, and the results are averaged with respect to the H and D distribution functions. The resulting differences in the zero-point averaged chemical shifts are compared with experimental values of the H/D shifts for a series of cycloalkanes, norbornane, adamantane, and protoadamantane. Agreement is generally very good. The remaining differences are discussed. The proton spectrum of cyclohexane- is revisited and updated with improved agreement with experiment.

The attachment system in fledgling relationships: an activating role for attachment anxiety.

PubMed

Eastwick, Paul W; Finkel, Eli J

2008-09-01

Is it sensible to study attachment dynamics between potential romantic partners before they share a full-fledged attachment bond? The present data indicate that such an approach may reveal novel insights about initial attraction processes. Four studies suggest that the state-like experience of attachment anxiety has functional implications within fledgling (i.e., desired or undeveloped) romantic relationships, well before the formation of an attachment bond. Studies 1 and 3 reveal that attachment anxiety directed toward a particular romantic interest is elevated before (in comparison with after) participants report being in an established relationship. Studies 2 and 3 demonstrate that such partner-specific attachment anxiety predicts attachment-relevant outcomes in fledgling relationships, including proximity seeking, safe haven, secure base, passionate love, and other approach behaviors. These associations were reliable above and beyond (and were typically as strong as or stronger than) the effect of sexual desire. Finally, Study 4 presents evidence that partner-specific attachment anxiety may cause several of these attachment-relevant outcomes. Attachment anxiety seems to be a normative experience and may signal the activation of the attachment system during the earliest stages of romantic relationships.

Silicon Hard-Stop Mesas for 3D Integration of Superconducting Qubits

NASA Astrophysics Data System (ADS)

Kim, David; Rosenberg, Danna; Osadchy, Brenda; Calusine, Greg; Das, Rabindra; Melville, Alexander; Yoder, Jonilyn; Yost, Donna-Ruth; Racz, Livia; Oliver, William

As quantum computing with superconducting qubits advances past the few-qubit stage, implementing 3D packaging/integration to route readout/control lines will become increasingly important. One approach is to bond chips that perform different functions using indium bump bonds. Because indium is malleable, however, achieving the desired spacing and tilt between two chips can be challenging. We present an approach based on etching several microns into the silicon substrate to produce hard stop silicon posts. Since this process involves etching into a pristine substrate, it is essential to evaluate its impact on qubit performance. We report the etched surface's effect on the resonator quality factor and qubit coherence time, as well as the improvement in planarity and tilt. This research was funded in part by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA) and by the Assistant Secretary of Defense for Research & Engineering under Air Force Contract No. FA8721-05-C-0002. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of ODNI, IARPA, or the US Government.

A self-healing PDMS polymer with solvatochromic properties.

PubMed

Jia, Xiao-Yong; Mei, Jin-Feng; Lai, Jian-Cheng; Li, Cheng-Hui; You, Xiao-Zeng

2015-05-28

Coordination bonds are effective for constructing functional self-healing materials due to their tunable bond strength and metal-ion-induced functionalities. In this work, we incorporate a cobalt(II) triazole complex into a polydimethylsiloxane (PDMS) matrix. The resulting polymers show solvatochromic behaviour as well as self-healing properties.

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.

Evolutionary perspectives on stress and affective disorder.

PubMed

Gardner, R

2001-01-01

Three general approaches to evolutionary perspectives in psychiatry include the following domains. (1) information from general medicine and physiology that involves defenses against infectious disease and predators, with obsessive compulsive disorder and posttraumatic stress disorder (PTSD) amongst the psychiatric results of this. (2) Sociophysiology assumes that normal brain functions mediate social interactions, including social rank hierarchy, in-out group formation, and family bonding. At times these function maladroitly resulting in psychiatric symptoms, for example, mania, persecutory delusions, and depression. (3) Evolutionary psychology explains self-sacrificing and generous behavior despite how genes act selfishly in natural selection theory, via the helping of relatives, reciprocal altruism, and manipulation of social contracts. Copyright 2001 by W.B. Saunders Company

FeF(3) catalyzed cascade C-C and C-N bond formation: synthesis of differentially substituted triheterocyclic benzothiazole functionalities under solvent-free condition.

PubMed

Atar, Amol B; Jeong, Yeon Tae

2014-05-01

A series of diverse polyfunctionalized triheterocyclic benzothiazoles were easily prepared in excellent yields via the Biginelli reaction of 2-aminobenzothiazole with substituted benzaldehydes and α-methylene ketones using FeF(3) as an expeditious catalyst under solvent-free conditions. The protocol provides a practical and straightforward approach toward highly functionalized triheterocyclic benzothiazole derivatives in excellent yields. The reaction was conveniently promoted by FeF(3) and the catalyst could be recovered easily after the reaction and reused without any loss of its catalytic activity. The advantageous features of this methodology are high atom economy, operational simplicity, shorter reaction time, convergence, and facile automation.

A theoretical investigation on bio-transformation of third generation anti-cancer drug Heptaplatin and its interaction with DNA purine bases

NASA Astrophysics Data System (ADS)

Reddy B., Venkata P.; Mukherjee, Subhajit; Mitra, Ishani; Moi, Sankar Ch.

2017-12-01

Heptaplatin is an approved platinum based cytostatic drug for the treatment of gastric cancers. The hydrolytic bio-transformation of Heptaplatin and the platination processes of guanine (G) and adenine (A) with resulting mono and di-aquated species of Heptaplatin have been investigated using density functional theory (DFT) combined with the conductor like dielectric continuum model (CPCM) approach, to spotlight the drug activation energy profiles and their binding mechanisms. The stationary points on the potential energy surfaces were fully optimized and characterized. The mono-functional binding of Heptaplatin, guanine as target over adenine due to electronic factors and more favorable hydrogen-bonds pattern.

Ab initio study of Fe(+)-benzyne

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1993-01-01

The interaction of Fe(+) with benzyne is studied using the self-consistent-field (SCF), complete active space SCF, and modified-coupled-pair functional levels of theory. The most stable structure is planar, where the Fe(+) has inserted into the in-plane pi bond, although the C-C bond distance suggests that some in-plane pi bonding remains. This system is compared with Sc(+) bonding to benzyne and other ligands.

Two different ways for waveguides and optoelectronics components on top of C-MOS

NASA Astrophysics Data System (ADS)

Fedeli, J. M.; Jeannot, S.; Kostrzewa, M.; Di Cioccio, L.; Jousseaume, V.; Orobtchouk, R.; Maury, P.; Zussy, M.

2006-02-01

While fabrication of photonic components at the wafer level is a long standing goal of integrated optics, new applications such as optical interconnects are introducing new challenges for waveguides and optoelectronic component fabrication. Indeed, global interconnects are expected to face severe limitations in the near future. To face this problem, optical links on top of a CMOS circuits could be an alternative. The critical points to perform an optical link on a chip are firstly the realization of compact passive optical distribution and secondly the report of optoelectronic components for the sources and detectors. This paper presents two different approaches for the integration of both waveguides and optoelectronic components. In a first "total bonding" approach, waveguides have been elaborated using classical "Silicon On Insulators" technology and then reported using molecular bonding on top off Si wafers. The S0I substrate was then chemically etched, after what InP dies were moleculary bonded on top of the waveguides. With this approach, optical components with low loses and a good equilibrium are demonsrated. Using molecular bonding, InP dies were reported with no degradation of the optoelectronic properties of the films. In a second approach, using PECVD silicon nitride or amorphous silicon coupled to PECVD silicon oxide, basic optical components are demonstrated. This low temperature technology is compatible with a microelectronic Back End process, allowing an integration of the waveguides directly on top of CMOS circuits. InP dies can then be bonded on top of the waveguides.

Multifunctional chondroitin sulphate for cartilage tissue-biomaterial integration

NASA Astrophysics Data System (ADS)

Wang, Dong-An; Varghese, Shyni; Sharma, Blanka; Strehin, Iossif; Fermanian, Sara; Gorham, Justin; Fairbrother, D. Howard; Cascio, Brett; Elisseeff, Jennifer H.

2007-05-01

A biologically active, high-strength tissue adhesive is needed for numerous medical applications in tissue engineering and regenerative medicine. Integration of biomaterials or implants with surrounding native tissue is crucial for both immediate functionality and long-term performance of the tissue. Here, we use the biopolymer chondroitin sulphate (CS), one of the major components of cartilage extracellular matrix, to develop a novel bioadhesive that is readily applied and acts quickly. CS was chemically functionalized with methacrylate and aldehyde groups on the polysaccharide backbone to chemically bridge biomaterials and tissue proteins via a twofold covalent link. Three-dimensional hydrogels (with and without cells) bonded to articular cartilage defects. In in vitro and in vivo functional studies this approach led to mechanical stability of the hydrogel and tissue repair in cartilage defects.

Coupling chemical and biological catalysis: a flexible paradigm for producing biobased chemicals.

PubMed

Schwartz, Thomas J; Shanks, Brent H; Dumesic, James A

2016-04-01

Advances in metabolic engineering have allowed for the development of new biological catalysts capable of selectively de-functionalizing biomass to yield platform molecules that can be upgraded to biobased chemicals using high efficiency continuous processing allowed by heterogeneous chemical catalysis. Coupling these disciplines overcomes the difficulties of selectively activating COH bonds by heterogeneous chemical catalysis and producing petroleum analogues by biological catalysis. We show that carboxylic acids, pyrones, and alcohols are highly flexible platforms that can be used to produce biobased chemicals by this approach. More generally, we suggest that molecules with three distinct functionalities may represent a practical upper limit on the extent of functionality present in the platform molecules that serve as the bridge between biological and chemical catalysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiscale Modeling of Thermal Conductivity of Polymer/Carbon Nanocomposites

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Frankland, Sarah-Jane V.; Hinkley, Jeffrey A.; Gates, Thomas S.

2010-01-01

Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between nanoparticles and amorphous and crystalline polymer matrices. Bulk thermal conductivities of the nanocomposites were then estimated using an established effective medium approach. To study functionalization, oligomeric ethylene-vinyl alcohol copolymers were chemically bonded to a single wall carbon nanotube. The results, in a poly(ethylene-vinyl acetate) matrix, are similar to those obtained previously for grafted linear hydrocarbon chains. To study the effect of noncovalent functionalization, two types of polyethylene matrices. -- aligned (extended-chain crystalline) vs. amorphous (random coils) were modeled. Both matrices produced the same interfacial thermal resistance values. Finally, functionalization of edges and faces of plate-like graphite nanoparticles was found to be only modestly effective in reducing the interfacial thermal resistance and improving the composite thermal conductivity

Adaptive polymeric nanomaterials utilizing reversible covalent and hydrogen bonding

NASA Astrophysics Data System (ADS)

Neikirk, Colin

Adaptive materials based on stimuli responsive and reversible bonding moieties are a rapidly developing area of materials research. Advances in supramolecular chemistry are now being adapted to novel molecular architectures including supramolecular polymers to allow small, reversible changes in molecular and nanoscale structure to affect large changes in macroscale properties. Meanwhile, dynamic covalent chemistry provides a complementary approach that will also play a role in the development of smart adaptive materials. In this thesis, we present several advances to the field of adaptive materials and also provide relevant insight to the areas of polymer nanocomposites and polymer nanoparticles. First, we have utilized the innate molecular recognition and binding capabilities of the quadruple hydrogen bonding group ureidopyrimidinone (UPy) to prepare supramolecular polymer nanocomposites based on supramolecular poly(caprolactone) which show improved mechanical properties, but also an increase in particle aggregation with nanoparticle UPy functionalization. We also present further insight into the relative effects of filler-filler, filler-matrix, and matrix-matrix interactions using a UPy side-chain functional poly(butyl acrylate). These nanocomposites have markedly different behavior depending on the amount of UPy sidechain functionality. Meanwhile, our investigations of reversible photo-response showed that coumarin functionality in polymer nanoparticles not only facilitates light mediated aggregation/dissociation behavior, but also provides a substantial overall reduction in particle size and improvement in nanoparticle stability for particles prepared by Flash NanoPrecipitation. Finally, we have combined these stimuli responsive motifs as a starting point for the development of multiresponsive adaptive materials. The synthesis of a library of multifunctional materials has provided a strong base for future research in this area, although our initial investigations were ultimately unsuccessful due to photodegradation of the UPy moiety in chloroform solution. This thesis has provided the Priestley lab with a solid base for the further investigation of the diverse applications and unsolved science of stimuli responsive adaptive materials.

Understanding Chemistry: Current and Possible

ERIC Educational Resources Information Center

Sanderson, R. T.

1976-01-01

Describes an instructional approach for teaching the cause-and-effect relationship between the qualities of atoms and the properties of their chemical compositions. Discusses atomic structure, ionization energies, homonuclear and heteronuclear bonding, and bond dissociation. (MLH)

Tug-of-war between classical and multicenter bonds in H-(Be)n-H species

NASA Astrophysics Data System (ADS)

Lundell, Katie A.; Boldyrev, Alexander I.

2018-05-01

Quantum chemical calculations were performed for beryllium homocatenated compounds [H-(Be)n-H]. Global minimum structures were found using machine searches (Coalescence Kick method) with density functional theory. Chemical bonding analysis was performed with the Adaptive Natural Density Partitioning method. It was found that H-(Be)2-H and H-(Be)3-H clusters are linear with classical two-center two-electron bonds, while for n > 3, three-dimensional structures are more stable with multicenter bonding. Thus, at n = 4, multicenter bonding wins the tug-of-war vs. the classical bonding.

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.

Natural bond orbital analysis, electronic structure, non-linear properties and vibrational spectral analysis of L-histidinium bromide monohydrate: a density functional theory.

PubMed

Sajan, D; Joseph, Lynnette; Vijayan, N; Karabacak, M

2011-10-15

The spectroscopic properties of the crystallized nonlinear optical molecule L-histidinium bromide monohydrate (abbreviated as L-HBr-mh) have been recorded and analyzed by FT-IR, FT-Raman and UV techniques. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability of the crystal were calculated with the help of density functional theory computations. The optimized geometric bond lengths and bond angles obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The natural bond orbital (NBO) analysis confirms the occurrence of strong intra and intermolecular N-H⋯O hydrogen bonding. Copyright © 2011 Elsevier B.V. All rights reserved.

SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals

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

Khabibullin, A.R.; Woods, L.M.; Karolak, A.

2016-06-15

Purpose: Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio-nuclei. Methods: The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab-initio Simulation Package (VASP) with the projector-augmented wave method and a plane-wave basis setmore » in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin-Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated. Results: Calculated binding energies for DOTA-radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF). Conclusion: DOTA-Gd, DOTA-Ac and DOTA-Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA-based-radiopharmaceuticals and will enhance our understanding of processes occurring at subatomic levels.« less

Shearography for Non-destructive Inspection with applications to BAT Mask Tile Adhesive Bonding and Specular Surface Honeycomb Panels

NASA Technical Reports Server (NTRS)

Lysak, Daniel B.

2003-01-01

The applicability of shearography techniques for non-destructive evaluation in two unique application areas is examined. In the first application, shearography is used to evaluate the quality of adhesive bonds holding lead tiles to the B.4T gamma ray mask for the NASA Swift program. Using a vibration excitation, the more poorly bonded tiles are readily identifiable in the shearography image. A quantitative analysis is presented that compares the shearography results with a destructive pull test measuring the force at bond failure. The second application is to evaluate the bonding between the skin and core of a honeycomb structure with a specular (mirror-like) surface. In standard shearography techniques, the object under test must have a diffuse surface to generate the speckle patterns in laser light, which are then sheared. A novel configuration using the specular surface as a mirror to image speckles from a diffuser is presented, opening up the use of shearography to a new class of objects that could not have been examined with the traditional approach. This new technique readily identifies large scale bond failures in the panel, demonstrating the validity of this approach.

A four-component coupling reaction of carbon dioxide, amines, cyclic ethers and 3-triflyloxybenzynes for the synthesis of functionalized carbamates.

PubMed

Xiong, Wenfang; Qi, Chaorong; Cheng, Ruixiang; Zhang, Hao; Wang, Lu; Yan, Donghao; Jiang, Huanfeng

2018-04-27

A novel four-component coupling reaction of carbon dioxide, amines, cyclic ethers and 3-triflyloxybenzynes has been developed for the first time, providing an efficient method for the synthesis of a series of functionalized carbamate derivatives in moderate to high yields. The process proceeds under mild, transition metal-free and fluoride-free conditions, leading to the formation of two new C-O bonds, one new C-N bond and one C-H bond in a single step.

Nickel(0)-Catalyzed Inert C-O Bond Functionalization: Organo Rare-Earth Metal Complex as the Coupling Partner.

PubMed

Yan, Xiangqian; Yang, Fanzhi; Cai, Guilong; Meng, Qingwei; Li, Xiaofang

2018-02-02

An organo rare-earth metal complex has been employed as a highly efficient nucleophile in Ni(0)-catalyzed C-O bond functionalization. The optimized catalytic system which consists of Ni(cod) 2 , PCy 3 , and t-BuONa could smoothly convert 1 equiv of naphthyl ethers to alkylated naphthalene analogues with 0.4 equiv of Ln(CH 2 SiMe 3 ) 3 (THF) 2 , delivering good to excellent yields. The reaction system could also activate the ArCH 2 -O bond with mild base.

Quantifying effects of cyclic stretch on cell-collagen substrate adhesiveness of vascular endothelial cells.

PubMed

Omidvar, Ramin; Tafazzoli-Shadpour, Mohammad; Mahmoodi-Nobar, Farbod; Azadi, Shohreh; Khani, Mohammad-Mehdi

2018-05-01

Vascular endothelium is continuously subjected to mechanical stimulation in the form of shear forces due to blood flow as well as tensile forces as a consequence of blood pressure. Such stimuli influence endothelial behavior and regulate cell-tissue interaction for an optimized functionality. This study aimed to quantify influence of cyclic stretch on the adhesive property and stiffness of endothelial cells. The 10% cyclic stretch with frequency of 1 Hz was applied to a layer of endothelial cells cultured on a polydimethylsiloxane substrate. Cell-substrate adhesion of endothelial cells was examined by the novel approach of atomic force microscope-based single-cell force spectroscopy and cell stiffness was measured by atomic force microscopy. Furthermore, the adhesive molecular bonds were evaluated using modified Hertz contact theory. Our results show that overall adhesion of endothelial cells with substrate decreased after cyclic stretch while they became stiffer. Based on the experimental results and theoretical modeling, the decrease in the number of molecular bonds after cyclic stretch was quantified. In conclusion, in vitro cyclic stretch caused alterations in both adhesive capacity and elastic modulus of endothelial cells through mechanotransductive pathways as two major determinants of the function of these cells within the cardiovascular system.

Studies toward the oxidative and reductive activation of C-S bonds in 2'-S-aryl-2'-thiouridine derivatives.

PubMed

Rayala, Ramanjaneyulu; Giuglio-Tonolo, Alain; Broggi, Julie; Terme, Thierry; Vanelle, Patrice; Theard, Patricia; Médebielle, Maurice; Wnuk, Stanislaw F

2016-04-21

Studies directed toward the oxidative and reductive desulfurization of readily available 2'- S -aryl-2'-thiouridine derivatives were investigated with the prospect to functionalize the C2'-position of nucleosides. The oxidative desulfurization-difluorination strategy was successful on 2-(arylthio)alkanoate surrogates, while extension of the combination of oxidants and fluoride sources was not an efficient fluorination protocol when applied to 2'- S -aryl-2'-thiouridine derivatives, resulting mainly in C5-halogenation of the pyrimidine ring and C2'-monofluorination without desulfurization. Cyclic voltammetry of 2'-arylsulfonyl-2'-deoxyuridines and their 2'-fluorinated analogues showed that cleavage of the arylsulfone moiety could occur, although at relatively high cathodic potentials. While reductive-desulfonylation of 2'-arylsulfonyl-2'-deoxyuridines with organic electron donors (OEDs) gave predominantly base-induced furan type products, chemical (OED) and electrochemical reductive-desulfonylation of the α-fluorosulfone derivatives yielded the 2'-deoxy-2'-fluorouridine and 2',3'-didehydro-2',3'-dideoxy-2'-fluorouridine derivatives. These results provided good evidence of the generation of a C2'-anion through carbon-sulfur bond cleavage, opening new horizons for the reductive-functionalization approaches in nucleosides.

Studies toward the oxidative and reductive activation of C-S bonds in 2'-S-aryl-2'-thiouridine derivatives

PubMed Central

Rayala, Ramanjaneyulu; Giuglio-Tonolo, Alain; Broggi, Julie; Terme, Thierry; Vanelle, Patrice; Theard, Patricia; Médebielle, Maurice; Wnuk, Stanislaw F.

2016-01-01

Studies directed toward the oxidative and reductive desulfurization of readily available 2'-S-aryl-2'-thiouridine derivatives were investigated with the prospect to functionalize the C2'-position of nucleosides. The oxidative desulfurization-difluorination strategy was successful on 2-(arylthio)alkanoate surrogates, while extension of the combination of oxidants and fluoride sources was not an efficient fluorination protocol when applied to 2'-S-aryl-2'-thiouridine derivatives, resulting mainly in C5-halogenation of the pyrimidine ring and C2'-monofluorination without desulfurization. Cyclic voltammetry of 2'-arylsulfonyl-2'-deoxyuridines and their 2'-fluorinated analogues showed that cleavage of the arylsulfone moiety could occur, although at relatively high cathodic potentials. While reductive-desulfonylation of 2'-arylsulfonyl-2'-deoxyuridines with organic electron donors (OEDs) gave predominantly base-induced furan type products, chemical (OED) and electrochemical reductive-desulfonylation of the α-fluorosulfone derivatives yielded the 2'-deoxy-2'-fluorouridine and 2',3'-didehydro-2',3'-dideoxy-2'-fluorouridine derivatives. These results provided good evidence of the generation of a C2'-anion through carbon-sulfur bond cleavage, opening new horizons for the reductive-functionalization approaches in nucleosides. PMID:27019535

Continuous Sound Velocity Measurements along the Shock Hugoniot Curve of Quartz

NASA Astrophysics Data System (ADS)

Li, Mu; Zhang, Shuai; Zhang, Hongping; Zhang, Gongmu; Wang, Feng; Zhao, Jianheng; Sun, Chengwei; Jeanloz, Raymond

2018-05-01

We report continuous measurements of the sound velocity along the principal Hugoniot curve of α quartz between 0.25 and 1.45 TPa, as determined from lateral release waves intersecting the shock front as a function of time in decaying-shock experiments. The measured sound velocities are lower than predicted by prior models, based on the properties of stishovite at densities below ˜7 g /cm3 , but agree with density functional theory molecular dynamics calculations and an empirical wide-regime equation of state presented here. The Grüneisen parameter calculated from the sound velocity decreases from γ ˜1 .3 at 0.25 TPa to 0.66 at 1.45 TPa. In combination with evidence for increased (configurational) specific heat and decreased bulk modulus, the values of γ suggest a high thermal expansion coefficient at ˜0. 25 - 0 .65 TPa , where SiO2 is thought to be a bonded liquid. From our measurements, dissociation of the molecular bonds persists to ˜0. 65 - 1 .0 TPa , consistent with estimates by other methods. At higher densities, the sound velocity is close to predictions from previous models, and the Grüneisen parameter approaches the ideal gas value.

Azobenzene versus 3,3',5,5'-tetra-tert-butyl-azobenzene (TBA) at Au(111): characterizing the role of spacer groups.

PubMed

McNellis, Erik R; Bronner, Christopher; Meyer, Jörg; Weinelt, Martin; Tegeder, Petra; Reuter, Karsten

2010-06-28

We present large-scale density-functional theory (DFT) calculations and temperature programmed desorption measurements to characterize the structural, energetic and vibrational properties of the functionalized molecular switch 3,3',5,5'-tetra-tert-butyl-azobenzene (TBA) adsorbed at Au(111). Particular emphasis is placed on exploring the accuracy of the semi-empirical dispersion correction approach to semi-local DFT (DFT-D) in accounting for the substantial van der Waals component in the surface bonding. In line with previous findings for benzene and pure azobenzene at coinage metal surfaces, DFT-D significantly overbinds the molecule, but seems to yield an accurate adsorption geometry as far as can be judged from the experimental data. Comparing the trans adsorption geometry of TBA and azobenzene at Au(111) reveals a remarkable insensitivity of the structural and vibrational properties of the -N[double bond, length as m-dash]N- moiety. This questions the established view of the role of the bulky tert-butyl-spacer groups for the switching of TBA in terms of a mere geometric decoupling of the photochemically active diazo-bridge from the gold substrate.

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.

Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

NASA Astrophysics Data System (ADS)

Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

2018-05-01

Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

Metal-metal bonding and aromaticity in [M2(NHCHNH)3]2 (μ-E)2 (E = O, S; M = Nb, Mo, Tc, Ru, Rh).

PubMed

Yan, Xiuli; Meng, Lingpeng; Sun, Zheng; Li, Xiaoyan

2016-02-01

The nature of M-M bonding and aromaticity of [M2(NHCHNH)3]2(μ-E)2 (E = O, S; M = Nb, Mo, Tc, Ru, Rh) was investigated using atoms in molecules (AIM) theory, electron localization function (ELF), natural bond orbital (NBO) and molecular orbital analysis. These analyses led to the following main conclusions: in [M2(NHCHNH)3]2(μ-E)2 (E = O, S; M = Nb, Mo, Tc, Ru, Rh), the Nb-Nb, Ru-Ru, and Rh-Rh bonds belong to "metallic" bonds, whereas Mo-Mo and Tc-Tc drifted toward the "dative" side; all these bonds are partially covalent in character. The Nb-Nb, Mo-Mo, and Tc-Tc bonds are stronger than Ru-Ru and Rh-Rh bonds. The M-M bonds in [M2(NHCHNH)3]2(μ-S)2 are stronger than those in [M2(NHCHNH)3]2(μ-O)2 for M = Nb, Mo, Tc, and Ru. The NICS(1)ZZ values show that all of the studied molecules, except [Ru2(NHCHNH)3]2(μ-O)2, are aromaticity molecules. O-bridged compounds have more aromaticity than S-bridged compounds. Graphical Abstract Left Molecular graph, and right electron localization function (ELF) isosurface of [M2(NHCHNH)3]2(μ-E)2(E = O, S; M = Nb, Mo, Tc, Ru, Rh).

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach

NASA Astrophysics Data System (ADS)

Suresh, D. M.; Amalanathan, M.; Sebastian, S.; Sajan, D.; Hubert Joe, I.; Bena Jothy, V.; Nemec, Ivan

2013-11-01

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction.

Low temperature InP /Si wafer bonding using boride treated surface

NASA Astrophysics Data System (ADS)

Huang, Hui; Ren, Xiaomin; Wang, Wenjuan; Song, Hailan; Wang, Qi; Cai, Shiwei; Huang, Yongqing

2007-04-01

An approach for InP /Si wafer bonding based on boride-solution treatment was presented. The bonding energy is higher than the InP fracture energy by annealing at 280°C. An In0.53Ga0.47As/InP multiple-quantum-well (MQW) structure grown on InP was transferred onto Si substrate via the bonding process. X-ray diffraction and photoluminescence reveal that crystal quality of the bonded MQW was preserved. A thin B2O3-POx-SiO2 oxide layer of about 28nm thick at the bonding interface was detected. X-ray photoelectron spectroscopy and Raman analyses indicate that the formation of oxygen bridging bonds by boride treatment is responsible for the strong fusion obtained at such low temperature.

Electron work function-a promising guiding parameter for material design.

PubMed

Lu, Hao; Liu, Ziran; Yan, Xianguo; Li, Dongyang; Parent, Leo; Tian, Harry

2016-04-14

Using nickel added X70 steel as a sample material, we demonstrate that electron work function (EWF), which largely reflects the electron behavior of materials, could be used as a guide parameter for material modification or design. Adding Ni having a higher electron work function to X70 steel brings more "free" electrons to the steel, leading to increased overall work function, accompanied with enhanced e(-)-nuclei interactions or higher atomic bond strength. Young's modulus and hardness increase correspondingly. However, the free electron density and work function decrease as the Ni content is continuously increased, accompanied with the formation of a second phase, FeNi3, which is softer with a lower work function. The decrease in the overall work function corresponds to deterioration of the mechanical strength of the steel. It is expected that EWF, a simple but fundamental parameter, may lead to new methodologies or supplementary approaches for metallic materials design or tailoring on a feasible electronic base.

Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.

PubMed

Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G

2014-09-16

Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.

FTIR spectroscopy as a tool for nano-material characterization

NASA Astrophysics Data System (ADS)

Baudot, Charles; Tan, Cher Ming; Kong, Jeng Chien

2010-11-01

Covalently grafting functional molecules to carbon nanotubes (CNTs) is an important step to leverage the excellent properties of that nano-fiber in order to exploit its potential in improving the mechanical and thermal properties of a composite material. While Fourier Transform Infra Red (FTIR) spectroscopy can display the various chemical bonding in a material, we found that the existing database in FTIR library does not cover all the bonding information present in functionalized CNTs because the bond between the grafted molecule and the CNT is new in the FTIR study. In order to extend the applicability of FTIR to nano-material, we present a theoretical method to derive FTIR spectroscopy and compare it with our experimental results. In particular, we illustrate a method for the identification of functional molecules grafted on CNTs, and we are able to confirm that the functional molecules are indeed covalently grafted on the CNTs without any alterations to its functional groups.

Dentin bond optimization using the dimethyl sulfoxide-wet bonding strategy: A 2-year in vitro study.

PubMed

Stape, Thiago Henrique Scarabello; Tjäderhane, Leo; Tezvergil-Mutluay, Arzu; Yanikian, Cristiane Rumi Fujiwara; Szesz, Anna Luiza; Loguercio, Alessandro Dourado; Martins, Luís Roberto Marcondes

2016-12-01

This study evaluated a new approach, named dimethyl sulfoxide (DMSO)-wet bonding, to produce more desirable long-term prospects for the ultrafine interactions between synthetic polymeric biomaterials and the inherently hydrated dentin substrate. Sound third molars were randomly restored with/without DMSO pretreatment using a total-etch (Scocthbond Multipurpose: SBMP) and a self-etch (Clearfil SE Bond: CF) adhesive systems. Restored teeth (n=10)/group were sectioned into sticks and submitted to different analyses: micro-Raman determined the degree of conversion inside the hybrid layer (DC); resin-dentin microtensile bond strength and fracture pattern analysis at 24h, 1year and 2 years of aging; and nanoleakage evaluation at 24h and 2 years. DMSO-wet bonding produced significantly higher 24h bond strengths for SBMP that were sustained over the two-year period, with significantly less adhesive failures. Similarly, DMSO-treated CF samples presented significantly higher bond strength than untreated samples at two years. Both adhesives had significant less adhesive failures at 2 years with DMSO. DMSO had no effect on DC of SBMP, but significantly increased the DC of CF. DMSO-treated SBMP samples presented reduced silver uptake compared to untreated samples after aging. Biomodification of the dentin substrate by the proposed strategy using DMSO is a suitable approach to produce more durable hybrid layers with superior ability to withstand hydrolytic degradation over time. Although the active role of DMSO on dentin bond improvement may vary according to monomer composition, its use seems to be effective on both self-etch and etch-and-rinse bonding mechanisms. Copyright © 2016 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

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.

Probing the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters by density functional calculations

NASA Astrophysics Data System (ADS)

Lu, Sheng-Jie

2018-05-01

We present a theoretical investigation on the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters using density functional theoretical calculations. The results showed that both anionic and neutral PtnC2 (n = 1-7) clusters primarily adopt 2D planar chain-shaped or ring-based structures. The two C atoms directly interact with each other to form a Csbnd C bond for n = 1-3, while the two C atoms are separated by the Pt atoms for n = 4-7, except for neutral Pt5C2. Pt4C2- anion and Pt4C2 neutral both show σ plus π double delocalized bonding patterns.

In-Depth Characterization of Protein Disulfide Bonds by Online Liquid Chromatography-Electrochemistry-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Switzar, Linda; Nicolardi, Simone; Rutten, Julie W.; Oberstein, Saskia A. J. Lesnik; Aartsma-Rus, Annemieke; van der Burgt, Yuri E. M.

2016-01-01

Disulfide bonds are an important class of protein post-translational modifications, yet this structurally crucial modification type is commonly overlooked in mass spectrometry (MS)-based proteomics approaches. Recently, the benefits of online electrochemistry-assisted reduction of protein S-S bonds prior to MS analysis were exemplified by successful characterization of disulfide bonds in peptides and small proteins. In the current study, we have combined liquid chromatography (LC) with electrochemistry (EC) and mass analysis by Fourier transform ion cyclotron resonance (FTICR) MS in an online LC-EC-MS platform to characterize protein disulfide bonds in a bottom-up proteomics workflow. A key advantage of a LC-based strategy is the use of the retention time in identifying both intra- and interpeptide disulfide bonds. This is demonstrated by performing two sequential analyses of a certain protein digest, once without and once with electrochemical reduction. In this way, the "parent" disulfide-linked peptide detected in the first run has a retention time-based correlation with the EC-reduced peptides detected in the second run, thus simplifying disulfide bond mapping. Using this platform, both inter- and intra-disulfide-linked peptides were characterized in two different proteins, ß-lactoglobulin and ribonuclease B. In order to prevent disulfide reshuffling during the digestion process, proteins were digested at a relatively low pH, using (a combination of) the high specificity proteases trypsin and Glu-C. With this approach, disulfide bonds in ß-lactoglobulin and ribonuclease B were comprehensively identified and localized, showing that online LC-EC-MS is a useful tool for the characterization of protein disulfide bonds.

QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations.

PubMed

Valdés-Martiní, José R; Marrero-Ponce, Yovani; García-Jacas, César R; Martinez-Mayorga, Karina; Barigye, Stephen J; Vaz d'Almeida, Yasser Silveira; Pham-The, Hai; Pérez-Giménez, Facundo; Morell, Carlos A

2017-06-07

In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify molecular information based on the bilinear, quadratic and linear algebraic forms and the graph-theoretical electronic-density and edge-adjacency matrices in order to consider atom- and bond-based relations, respectively. These MDs have been successfully applied in the screening of chemical compounds of different therapeutic applications ranging from antimalarials, antibacterials, tyrosinase inhibitors and so on. To compute these MDs, a computational program with the same name was initially developed. However, this in house software barely offered the functionalities required in contemporary molecular modeling tasks, in addition to the inherent limitations that made its usability impractical. Therefore, the present manuscript introduces the QuBiLS-MAS (acronym for Quadratic, Bilinear and N-Linear mapS based on graph-theoretic electronic-density Matrices and Atomic weightingS) software designed to compute topological (0-2.5D) molecular descriptors based on bilinear, quadratic and linear algebraic forms for atom- and bond-based relations. The QuBiLS-MAS module was designed as standalone software, in which extensions and generalizations of the former ToMoCoMD-CARDD 2D-algebraic indices are implemented, considering the following aspects: (a) two new matrix normalization approaches based on double-stochastic and mutual probability formalisms; (b) topological constraints (cut-offs) to take into account particular inter-atomic relations; (c) six additional atomic properties to be used as weighting schemes in the calculation of the molecular vectors; (d) four new local-fragments to consider molecular regions of interest; (e) number of lone-pair electrons in chemical structure defined by diagonal coefficients in matrix representations; and (f) several aggregation operators (invariants) applied over atom/bond-level descriptors in order to compute global indices. This software permits the parallel computation of the indices, contains a batch processing module and data curation functionalities. This program was developed in Java v1.7 using the Chemistry Development Kit library (version 1.4.19). The QuBiLS-MAS software consists of two components: a desktop interface (GUI) and an API library allowing for the easy integration of the latter in chemoinformatics applications. The relevance of the novel extensions and generalizations implemented in this software is demonstrated through three studies. Firstly, a comparative Shannon's entropy based variability study for the proposed QuBiLS-MAS and the DRAGON indices demonstrates superior performance for the former. A principal component analysis reveals that the QuBiLS-MAS approach captures chemical information orthogonal to that codified by the DRAGON descriptors. Lastly, a QSAR study for the binding affinity to the corticosteroid-binding globulin using Cramer's steroid dataset is carried out. From these analyses, it is revealed that the QuBiLS-MAS approach for atom-pair relations yields similar-to-superior performance with regard to other QSAR methodologies reported in the literature. Therefore, the QuBiLS-MAS approach constitutes a useful tool for the diversity analysis of chemical compound datasets and high-throughput screening of structure-activity data.

Application of the bond valence method in the non-isovalent semiconductor alloy (GaN) 1–x (ZnO) x

DOE PAGES

Liu, Jian

2016-09-29

This paper studies the bond valence method (BVM) and its application in the non-isovalent semiconductor alloy (GaN) 1-x(ZnO) x. Particular attention is paid to the role of short-range order (SRO). A physical interpretation based on atomic orbital interaction is proposed and examined by density-functional theory (DFT) calculations. Combining BVM with Monte-Carlo simulations and a DFT-based cluster expansion model, bond-length distributions and bond-angle variations are predicted. The correlation between bond valence and bond stiffness is also revealed. Lastly the concept of bond valence is extended into the modelling of an atomistic potential.

A new class of halogen bonds that avoids the σ-hole

NASA Astrophysics Data System (ADS)

Zhang, Yu; Ma, Ning; Wang, Weizhou

2012-04-01

A new class of halogen bonds of the type X = Hal⋯Y has been investigated by using the density functional theory calculations. The strength of this new class of halogen bonds is in the range of 90-120 kcal/mol, which is greatly larger than that of the conventional halogen bond of the type X-Hal⋯Y. The geometry of this new class of halogen bonds is not determined by the halogen's positive σ-hole. Natural bond orbital analysis shows it is the n → π∗ interaction that determines the geometry of this new class of halogen bonds. Experimental results are in good agreement with the theoretical predictions.

On the atomic structure of liquid Ni-Si alloys: a neutron diffraction study

NASA Astrophysics Data System (ADS)

Gruner, S.; Marczinke, J.; Hennet, L.; Hoyer, W.; Cuello, G. J.

2009-09-01

The atomic structure of the liquid NiSi and NiSi2 alloys is investigated by means of neutron diffraction experiments with isotopic substitution. From experimental data-sets obtained using four Ni isotopes, partial structure factors and pair correlation functions are obtained by applying a reverse Monte Carlo modelling approach. Both alloys were found to exhibit a strong tendency to hetero-coordination within the first coordination shell. In particular, covalent Si-Si bonds with somewhat greater distances seem to influence the structure of the liquid NiSi alloy.

On the atomic structure of liquid Ni-Si alloys: a neutron diffraction study.

PubMed

Gruner, S; Marczinke, J; Hennet, L; Hoyer, W; Cuello, G J

2009-09-23

The atomic structure of the liquid NiSi and NiSi(2) alloys is investigated by means of neutron diffraction experiments with isotopic substitution. From experimental data-sets obtained using four Ni isotopes, partial structure factors and pair correlation functions are obtained by applying a reverse Monte Carlo modelling approach. Both alloys were found to exhibit a strong tendency to hetero-coordination within the first coordination shell. In particular, covalent Si-Si bonds with somewhat greater distances seem to influence the structure of the liquid NiSi alloy.

First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

DOE PAGES

Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

2014-10-21

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1 b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation andmore » the dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.« less

Application of High-Impact Polystyrene (HIPS) as a Graphene Nanoparticle Reinforced Composite Thermoplastic Adhesive

NASA Astrophysics Data System (ADS)

Stitt, Erik

Adhesive bonding is a more efficient joining method for composites than traditional mechanical fasteners and provides advantages in weight reduction, simplicity, and cost. In addition, the utilization of mechanical fasteners introduces stress concentrations and damage to the fiber-matrix interface. Adhesive bonding with thermoset polymers distributes mechanical loads but also makes disassembly for repair and recycling difficult. The ability to utilize thermoplastic polymers as adhesives offers an approach to address these limitations and can even produce a reversible adhesive joining technology through combining conductive nanoparticles with a thermoplastic polymer. The incorporation of the conductive nanoparticles allows for selective heating of the adhesive via exposure to electromagnetic (EM) radiation and simultaneously can augment the mechanical properties of the adhesive and the adhesive joint. This approach provides a versatile mechanism for efficiently creating and reversing structural adhesive joints across a wide range of materials. In this work, a high-impact polystyrene (HIPS) co-polymer containing butadiene as a toughness modifier is compounded with graphene nano-platelets (GnP) for investigation as a thermoplastic adhesive. The properties of the bulk composite adhesive are tailored by altering the morphology, dispersion, and concentration of GnP. The thermal response of the material to EM radiation in the microwave frequency spectrum was investigated and optimized. Surface treatments of the adhesive films were explored to enhance the viability of this nanoparticle thermoplastic polymer to function as a reversible adhesive. As a result, it has been shown that lap-shear strengths of multi-material joints produced from aforementioned thermoplastic adhesives were comparable to similar thermoset bonded joints.

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.

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.

Open-Shell Lanthanide(II+) or -(III+) Complexes Bearing σ-Silyl and Silylene Ligands: Synthesis, Structure, and Bonding Analysis

PubMed Central

2015-01-01

Complexes featuring lanthanide (Ln)–Si bonds represent a highly neglected research area. Herein, we report a series of open-shell LnII+ and LnIII+ complexes bearing σ-bonded silyl and base-stabilized N-heterocyclic silylene (NHSi) ligands. The reactions of the LnIII+ complexes Cp3Ln (Ln = Tm, Ho, Tb, Gd; Cp = cyclopentadienide) with the 18-crown-6 (18-cr-6)-stabilized 1,4-oligosilanyl dianion [(18-cr-6)KSi(SiMe3)2SiMe2SiMe2Si(SiMe3)2K(18-cr-6)] (1) selectively afford the corresponding metallacyclopentasilane salts [Cp2Ln({Si(SiMe3)2SiMe2}2)]−[K2(18-cr-6)2Cp]+ [Ln = Tm (2a), Ho (2b), Tb (2c), Gd (2d)]. Complexes 2a–2d represent the first examples of structurally characterized Tm, Ho, Tb, and Gd complexes featuring Ln–Si bonds. Strikingly, the analogous reaction of 1 with the lighter element analogue Cp3Ce affords the acyclic product [Cp3CeSi(SiMe3)2SiMe2SiMe2Si(SiMe3)2-Cp3Ce]2–2[K(18-cr-6)]+ (3) as the first example of a complex featuring a Ce–Si bond. In an alternative synthetic approach, the aryloxy-functionalized benzamidinato NHSi ligand Si(OC6H4-2-tBu){(NtBu)2CPh} (4a) and the alkoxy analogue Si(OtBu){(NtBu)2CPh} (4b) were reacted with Cp*2Sm(OEt2), affording, by OEt2 elimination, the corresponding silylene complexes, both featuring SmII+ centers: Cp*2Sm ← :Si(O–C6H4-2-tBu){(NtBu)2CPh} (6) and Cp*2Sm ← :Si(OtBu){(NtBu)2CPh} (5). Complexes 5 and 6 are the first four-coordinate silylene complexes of any f-block element to date. All complexes were fully characterized by spectroscopic means and by single-crystal X-ray diffraction analysis. In the series 2a–2d, a linear correlation was observed between the Ln–Si bond lengths and the covalent radii of the corresponding Ln metals. Moreover, in complexes 5 and 6, notably long Sm–Si bonds are observed, in accordance with a donor–acceptor interaction between Si and Sm [5, 3.4396(15) Å; 6, 3.3142(18) Å]. Density functional theory calculations were carried out for complexes 2a–2d, 5, and 6 to elucidate the bonding situation between the LnII+ or LnIII+ centers and Si. In particular, a decrease in the Mayer bond order (MBO) of the Ln–Si bond is observed in the series 2a–2d in moving from the lighter to the heavier lanthanides (Tm = 0.53, Ho = 0.62, Tb = 0.65, and Gd = 0.75), which might indicate decreasing covalency in the Ln–Si bond. In accordance with the long bond lengths observed experimentally in complexes 5 and 6, comparatively low MBOs were determined for both silylene complexes (5, 0.24; 6, 0.25) . PMID:25756230

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

Temperature effect on the small-to-large crossover lengthscale of hydrophobic hydration

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

Djikaev, Y. S., E-mail: idjikaev@buffalo.edu; Ruckenstein, E.

2013-11-14

The thermodynamics of hydration is expected to change gradually from entropic for small solutes to enthalpic for large ones. The small-to-large crossover lengthscale of hydrophobic hydration depends on the thermodynamic conditions of the solvent such as temperature, pressure, presence of additives, etc. We attempt to shed some light on the temperature dependence of the crossover lengthscale by using a probabilistic approach to water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a solute and solute radius. Incorporating that approach into the densitymore » functional theory, one can examine the solute size effects on its hydration over the entire small-to-large lengthscale range at a series of different temperatures. Knowing the dependence of the hydration free energy on the temperature and solute size, one can also obtain its enthalpic and entropic contributions as functions of both temperature and solute size. These functions can provide some interesting insight into the temperature dependence of the crossover lengthscale of hydrophobic hydration. The model was applied to the hydration of spherical particles of various radii in water in the temperature range from T = 293.15 K to T = 333.15 K. The model predictions for the temperature dependence of the hydration free energy of small hydrophobes are consistent with the experimental and simulational data on the hydration of simple molecular solutes. Three alternative definitions for the small-to-large crossover length-scale of hydrophobic hydration are proposed, and their temperature dependence is obtained. Depending on the definition and temperature, the small-to-large crossover in the hydration mechanism is predicted to occur for hydrophobes of radii from one to several nanometers. Independent of its definition, the crossover length-scale is predicted to decrease with increasing temperature.« less

Chemical Bonding: The Orthogonal Valence-Bond View

PubMed Central

Sax, Alexander F.

2015-01-01

Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF) wave functions, these processes can be calculated, but the local information is hidden by the delocalized molecular orbitals (MO) used to construct the wave functions. The transformation of such wave functions into valence bond (VB) wave functions, which are based on localized orbitals, reveals the hidden information; this transformation is called a VB reading of MCSCF wave functions. The two-electron VB wave functions describing the Lewis electron pair that connects two atoms are frequently called covalent or neutral, suggesting that these wave functions describe an electronic situation where two electrons are never located at the same atom; such electronic situations and the wave functions describing them are called ionic. When the distance between two atoms decreases, however, every covalent VB wave function composed of non-orthogonal atomic orbitals changes its character from neutral to ionic. However, this change in the character of conventional VB wave functions is hidden by its mathematical form. Orthogonal VB wave functions composed of orthonormalized orbitals never change their character. When localized fragment orbitals are used instead of atomic orbitals, one can decide which local information is revealed and which remains hidden. In this paper, we analyze four chemical reactions by transforming the MCSCF wave functions into orthogonal VB wave functions; we show how the reactions are influenced by changing the atoms involved or by changing their local symmetry. Using orthogonal instead of non-orthogonal orbitals is not just a technical issue; it also changes the interpretation, revealing the properties of wave functions that remain otherwise undetected. PMID:25906476

Proceedings of the Second Annual Symposium for Nondestructive Evaluation of Bond Strength

NASA Technical Reports Server (NTRS)

Roberts, Mark J. (Compiler)

1999-01-01

Ultrasonics, microwaves, optically stimulated electron emission (OSEE), and computational chemistry approaches have shown relevance to bond strength determination. Nonlinear ultrasonic nondestructive evaluation methods, however, have shown the most effectiveness over other methods on adhesive bond analysis. Correlation to changes in higher order material properties due to microstructural changes using nonlinear ultrasonics has been shown related to bond strength. Nonlinear ultrasonic energy is an order of magnitude more sensitive than linear ultrasound to these material parameter changes and to acoustic velocity changes caused by the acoustoelastic effect when a bond is prestressed. Signal correlations between non-linear ultrasonic measurements and initialization of bond failures have been measured. This paper reviews bond strength research efforts presented by university and industry experts at the Second Annual Symposium for Nondestructive Evaluation of Bond Strength organized by the NDE Sciences Branch at NASA Langley in November 1998.

Conceptual DFT: the chemical relevance of higher response functions.

PubMed

Geerlings, P; De Proft, F

2008-06-07

In recent years conceptual density functional theory offered a perspective for the interpretation/prediction of experimental/theoretical reactivity data on the basis of a series of response functions to perturbations in the number of electrons and/or external potential. This approach has enabled the sharp definition and computation, from first principles, of a series of well-known but sometimes vaguely defined chemical concepts such as electronegativity and hardness. In this contribution, a short overview of the shortcomings of the simplest, first order response functions is illustrated leading to a description of chemical bonding in a covalent interaction in terms of interacting atoms or groups, governed by electrostatics with the tendency to polarize bonds on the basis of electronegativity differences. The second order approach, well known until now, introduces the hardness/softness and Fukui function concepts related to polarizability and frontier MO theory, respectively. The introduction of polarizability/softness is also considered in a historical perspective in which polarizability was, with some exceptions, mainly put forward in non covalent interactions. A particular series of response functions, arising when the changes in the external potential are solely provoked by changes in nuclear configurations (the "R-analogues") are also systematically considered. The main part of the contribution is devoted to third order response functions which, at first sight, may be expected not to yield chemically significant information, as turns out to be for the hyperhardness. A counterexample is the dual descriptor and its R analogue, the initial hardness response, which turns out to yield a firm basis to regain the Woodward-Hoffmann rules for pericyclic reactions based on a density-only basis, i.e. without involving the phase, sign, symmetry of the wavefunction. Even the second order nonlinear response functions are shown possibly to bear interesting information, e.g. on the local and global polarizability. Its derivatives may govern the influence of charge on the polarizability, the R-analogues being the nuclear Fukui function and the quadratic and cubic force constants. Although some of the higher order derivatives may be difficult to evaluate a comparison with the energy expansion used in spectroscopy in terms of nuclear displacements, nuclear magnetic moments, electric and magnetic fields leads to the conjecture that, certainly cross terms may contain new, intricate information for understanding chemical reactivity.

Combined surface activated bonding using H-containing HCOOH vapor treatment for Cu/Adhesive hybrid bonding at below 200 °C

NASA Astrophysics Data System (ADS)

He, Ran; Fujino, Masahisa; Akaike, Masatake; Sakai, Taiji; Sakuyama, Seiki; Suga, Tadatomo

2017-08-01

Cu/adhesive hybrid bonding is an attractive approach to three-dimensional (3D) integration because it provides direct Cusbnd Cu vertical interconnects and high mechanical stability. However, Cu/adhesive hybrid bonding at below 200 °C is still challenging because of bonding temperature mismatch between Cusbnd Cu and polymer adhesives and lacking of effective adhesive-compatible Cu surface activation methods. In this paper, we investigate and demonstrate a ;Cu-first; hybrid bonding technique by using hydrogen(H)-containing formic acid (HCOOH) vapor prebonding surface treatment for the first time. In this technique, high-quality Cusbnd Cu bonding is obtained at 180-200 °C that is close to or even lower than the temperature of subsequent adhesive curing. We experimentally investigate the effects of the H-containing HCOOH vapor treatment for Cusbnd Cu bonding and cyclo-olefin polymer adhesive-adhesive bonding. This technique enables Cu/adhesive hybrid bonding at below 200 °C, promising smaller thermal stress, higher throughput, and lower cost comparing to the existing ;adhesive-first; hybrid bonding method.

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.

Functional Smiles: Tools for Love, Sympathy, and War.

PubMed

Rychlowska, Magdalena; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Martin, Jared D; Niedenthal, Paula M

2017-09-01

A smile is the most frequent facial expression, but not all smiles are equal. A social-functional account holds that smiles of reward, affiliation, and dominance serve basic social functions, including rewarding behavior, bonding socially, and negotiating hierarchy. Here, we characterize the facial-expression patterns associated with these three types of smiles. Specifically, we modeled the facial expressions using a data-driven approach and showed that reward smiles are symmetrical and accompanied by eyebrow raising, affiliative smiles involve lip pressing, and dominance smiles are asymmetrical and contain nose wrinkling and upper-lip raising. A Bayesian-classifier analysis and a detection task revealed that the three smile types are highly distinct. Finally, social judgments made by a separate participant group showed that the different smile types convey different social messages. Our results provide the first detailed description of the physical form and social messages conveyed by these three types of functional smiles and document the versatility of these facial expressions.

Engineering responsive supramolecular biomaterials: Toward smart therapeutics.

PubMed

Webber, Matthew J

2016-09-01

Engineering materials using supramolecular principles enables generalizable and modular platforms that have tunable chemical, mechanical, and biological properties. Applying this bottom-up, molecular engineering-based approach to therapeutic design affords unmatched control of emergent properties and functionalities. In preparing responsive materials for biomedical applications, the dynamic character of typical supramolecular interactions facilitates systems that can more rapidly sense and respond to specific stimuli through a fundamental change in material properties or characteristics, as compared to cases where covalent bonds must be overcome. Several supramolecular motifs have been evaluated toward the preparation of "smart" materials capable of sensing and responding to stimuli. Triggers of interest in designing materials for therapeutic use include applied external fields, environmental changes, biological actuators, applied mechanical loading, and modulation of relative binding affinities. In addition, multistimuli-responsive routes can be realized that capture combinations of triggers for increased functionality. In sum, supramolecular engineering offers a highly functional strategy to prepare responsive materials. Future development and refinement of these approaches will improve precision in material formation and responsiveness, seek dynamic reciprocity in interactions with living biological systems, and improve spatiotemporal sensing of disease for better therapeutic deployment.

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.

Theoretical Study of Fe(CO)n-

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Baushlicher, Charles W., Jr.

1995-01-01

The structures and CO binding energies are computed for Fe(CO)n- using a hybrid density functional theory (DFT) approach. The structures and ground states can be explained in terms of maximizing the Fe to CO 2pi* donation and minimizing Fe-CO 5 sigma repulsion. The trends in the CO binding energies for Fe(CO)n- and the differences between the trends for Fe(CO)n- and Fe(CO)n are also explained. For Fe(CO)n-, the second, third, and fourth CO bonding energies are in good agreement with experiment, while the first is too small. The first CO binding is also too small using the coupled cluster singles and doubles approach including a perturbation estimate of the connected triple excitations.

First principles prediction of amorphous phases using evolutionary algorithms

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

Nahas, Suhas, E-mail: shsnhs@iitk.ac.in; Gaur, Anshu, E-mail: agaur@iitk.ac.in; Bhowmick, Somnath, E-mail: bsomnath@iitk.ac.in

2016-07-07

We discuss the efficacy of evolutionary method for the purpose of structural analysis of amorphous solids. At present, ab initio molecular dynamics (MD) based melt-quench technique is used and this deterministic approach has proven to be successful to study amorphous materials. We show that a stochastic approach motivated by Darwinian evolution can also be used to simulate amorphous structures. Applying this method, in conjunction with density functional theory based electronic, ionic and cell relaxation, we re-investigate two well known amorphous semiconductors, namely silicon and indium gallium zinc oxide. We find that characteristic structural parameters like average bond length and bondmore » angle are within ∼2% of those reported by ab initio MD calculations and experimental studies.« less