Broadband Microwave Spectroscopy as a Tool to Study Dispersion Interactions in Camphor-Alcohol Systems

NASA Astrophysics Data System (ADS)

Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie

2016-06-01

Many biological processes such as chemical recognition and protein folding are mainly controlled by the interplay between hydrogen bonds and dispersive forces. Broadband rotational spectroscopy studies of weakly bound complexes are able to accurately reveal the structures and internal dynamics of molecular clusters isolated in the gas phase. To investigate the influence of the interplay between different types of weak intermolecular interactions and how it controls the preferred active sites of an amphiphilic molecule, we are using camphor (C10H16O, 1,7,7-trimethylbicyclo[2.2.1]hepta-2-one) with different aliphatic alcohol systems. Camphor is a conformationally rigid bicyclic molecule endowed with considerable steric hindrance and has a single polar group (-C=O). The rotational spectrum of camphor and its structure has been previously reported [1] as well as multiple clusters with water [2]. In order to determine the structure of the camphor-alcohol complexes, we targeted low energy rotational transitions in the 2-8 GHz range under the isolated conditions of a molecular jet in the gas phase. The data obtained suggests that camphor forms one complex with methanol and two with ethanol, with differences in the intermolecular interaction in both complexes. With these results, we aim to study the shift in intermolecular interaction from hydrogen bonding to dispersion with the increase in the size of the aliphatic alcohol. [1] Z. Kisiel, et al., Phys. Chem. Chem. Phys., 5 (2003), 820-826. [2] C. Pérez, et al, J. Phys. Chem. Lett., 7 (2016), 154-160.

Intermolecular interactions between imidazole derivatives intercalated in layered solids. Substituent group effect

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

González, M.; Lemus-Santana, A.A.; Rodríguez-Hernández, J.

2013-08-15

This study sheds light on the intermolecular interactions between imidazole derive molecules (2-methyl-imidazole, 2-ethyl-imidazole and benzimidazole) intercalated in T[Ni(CN){sub 4}] layers to form a solid of formula unit T(ImD){sub 2}[Ni(CN){sub 4}]. These hybrid inorganic–organic solids were prepared by soft chemical routes and their crystal structures solved and refined from X-ray powder diffraction data. The involved imidazole derivative molecules were found coordinated through the pyridinic N atom to the axial positions for the metal T in the T[Ni(CN){sub 4}] layer. In the interlayers region ligand molecules from neighboring layers remain stacked in a face-to-face configuration through dipole–dipole and quadrupole–quadrupole interactions. Thesemore » intermolecular interactions show a pronounced dependence on the substituent group and are responsible for an ImD-pillaring concatenation of adjacent layers. This is supported by the structural information and the recorded magnetic data in the 2–300 K temperature range. The samples containing Co and Ni are characterized by presence of spin–orbit coupling and pronounced temperature dependence for the effective magnetic moment except for 2-ethyl-imidazole related to the local distortion for the metal coordination environment. For this last one ligand a weak ferromagnetic ordering ascribed to a super-exchange interaction between T metals from neighboring layers through the ligands π–π interaction was detected. - Graphical abstract: In the interlayers region imidazole derivative molecules are oriented according to their dipolar and quadrupolar interactions and minimizing the steric impediment. Highlights: • Imidazole derivatives intercalation compounds. • Intermolecular interaction between intercalated imidazole derivatives. • Hybrid inorganic–organic solids. • Pi–pi interactions and ferromagnetic coupling. • Dipolar and quadrupolar interactions between intercalated imidazole derivatives.« less

Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines

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

Dou, Wei-Dong; Center of Super-Diamond and Advanced Films; Huang, Shu-Ping

2015-10-07

Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π–π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc andmore » CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.« less

Greenhouse effect in planetary atmospheres caused by molecular symmetry breaking in intermolecular interactions

NASA Astrophysics Data System (ADS)

Vigasin, A. A.; Mokhov, I. I.

2017-03-01

It is believed that the greenhouse effect is related to the parameters of absorption spectra of polyatomic molecules, usually trace gases, in planetary atmospheres. The main components of all known atmospheres of celestial bodies are symmetrical molecules that do not possess the dipole-allowed purely rotational (and in the case of diatomic molecules, vibrational-rotational) absorption spectrum. Upon increased pressure, a weak absorption appears, induced by intermolecular interaction, which can lead to a greenhouse effect. The contribution of the induced absorption in radiative forcing of a dense atmosphere may amount to a few or even tens of W/m2. In conditions typical for the atmospheres of terrestrial planets (including paleoatmospheres), the collision-induced absorption and associated greenhouse effect may lead to an increase in surface temperature above the freezing point of water. There is a correlation between the temperature of an atmosphere and the intermolecular bonding energy of gases that dominate in planetary atmospheres of the Solar System.

High strength films from oriented, hydrogen-bonded "graphamid" 2D polymer molecular ensembles.

PubMed

Sandoz-Rosado, Emil; Beaudet, Todd D; Andzelm, Jan W; Wetzel, Eric D

2018-02-27

The linear polymer poly(p-phenylene terephthalamide), better known by its tradename Kevlar, is an icon of modern materials science due to its remarkable strength, stiffness, and environmental resistance. Here, we propose a new two-dimensional (2D) polymer, "graphamid", that closely resembles Kevlar in chemical structure, but is mechanically advantaged by virtue of its 2D structure. Using atomistic calculations, we show that graphamid comprises covalently-bonded sheets bridged by a high population of strong intermolecular hydrogen bonds. Molecular and micromechanical calculations predict that these strong intermolecular interactions allow stiff, high strength (6-8 GPa), and tough films from ensembles of finite graphamid molecules. In contrast, traditional 2D materials like graphene have weak intermolecular interactions, leading to ensembles of low strength (0.1-0.5 GPa) and brittle fracture behavior. These results suggest that hydrogen-bonded 2D polymers like graphamid would be transformative in enabling scalable, lightweight, high performance polymer films of unprecedented mechanical performance.

Surface-enhanced Raman scattering on molecular self-assembly in nanoparticle-hydrogel composite.

PubMed

Miljanić, Snezana; Frkanec, Leo; Biljan, Tomislav; Meić, Zlatko; Zinić, Mladen

2006-10-24

Surface-enhanced Raman scattering has been applied to study weak intermolecular interactions between small organic gelling molecules involved in the silver nanoparticle-hydrogel composite formation. Assembly and disassembly of the gelator molecules in close vicinity to embedded silver nanoparticles were followed by changes in Raman intensity of the amide II and carboxyl vibrational bands, whereas the strength of the bands related to benzene modes remained constant. This implied that the gelator molecules were strongly attached to the silver particles through the benzene units, while participating in gel structure organization by intermolecular hydrogen bonding between oxalyl amide and carboxyl groups.

Molecular self-recognition: a chiral [Mn(II)6] wheel via donor-acceptor π···π contacts and H-bonds.

PubMed

Barrios, L A; Salinas-Uber, J; Roubeau, O; Teat, S J; Aromí, G

2015-03-18

A multinucleating ligand capable of establishing different types of intermolecular interactions, when combined with acetate groups leads to the assembly of a chiral [Mn(II)3] cluster poised for a process of self-recognition through a combination of perfectly complementary weak forces.

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

DOE PAGES

Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; ...

2015-08-14

Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically,more » the presence of C π...C πinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.« less

Broadband Microwave Spectroscopy as a Tool to Study Intermolecular Interactions in the Diphenyl Ether - Water System

NASA Astrophysics Data System (ADS)

Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie

2017-06-01

Many biological processes, such as chemical recognition and protein folding, are mainly controlled by the interplay of hydrogen bonds and dispersive forces. This interplay also occurs between organic molecules and solvent water molecules. Broadband rotational spectroscopy studies of weakly bound complexes are able to accurately reveal the structures and internal dynamics of molecular clusters isolated in the gas phase. Amongst them, water clusters with organic molecules are of particular interest. In this work, we investigate the interplay between different types of weak intermolecular interactions and how it controls the preferred interaction sites of aromatic ethers, where dispersive interactions may play a significant role. We present our results on diphenyl ether (C_{12}H_{10}O, 1,1'-Oxydibenzene) complexed with up to three molecules of water. Diphenyl ether is a flexible molecule, and it offers two competing binding sites for water: the ether oxygen and the aromatic π system. In order to determine the structure of the diphenyl ether-water complexes, we targeted transitions in the 2-8 GHz range using broadband rotational spectroscopy. We identify two isomers with one water, one with two water, and one with three water molecules. Further analysis from isotopic substitution measurements provided accurate structural information. The preferred interactions, as well as the observed structural changes induced upon complexation, will be presented and discussed.

Photoinduced charge-transfer electronic excitation of tetracyanoethylene/tetramethylethylene complex in dichloromethane

NASA Astrophysics Data System (ADS)

Xu, Long-Kun; Bi, Ting-Jun; Ming, Mei-Jun; Wang, Jing-Bo; Li, Xiang-Yuan

2017-07-01

Based on the previous work on nonequilibrium solvation model by the authors, Intermolecular charge-transfer electronic excitation of tetracyanoethylene (TCE)/tetramethylethylene (TME) π -stacked complex in dichloromethane (DCM) has been investigated. For weak interaction correction, dispersion corrected functional DFT-D3 is adopted for geometry optimization. In order to identify the excitation metric, dipole moment components of each Cartesian direction, atomic charge, charge separation and Δr index are analyzed for TCE/TME complex. Calculation shows that the calculated excitation energy is dependent on the functional choice, when conjuncted with suitable time-dependent density functional, the modified nonequilibrium expression gives satisfied results for intermolecular charge-transfer electronic excitation.

Self-assembly of acetate adsorbates drives atomic rearrangement on the Au(110) surface

DOE PAGES

Hiebel, Fanny; Shong, Bonggeun; Chen, Wei; ...

2016-10-12

Weak inter-adsorbate interactions are shown to play a crucial role in determining surface structure, with major implications for its catalytic reactivity. This is exemplified here in the case of acetate bound to Au(110), where the small extra energy of the van der Waals interactions among the surface-bound groups drives massive restructuring of the underlying Au. Acetate is a key intermediate in electro-oxidation of CO 2 and a poison in partial oxidation reactions. Metal atom migration originates at surface defects and is likely facilitated by weakened Au–Au interactions due to bonding with the acetate. Even though the acetate is a relativelymore » small molecule, weak intermolecular interaction provides the energy required for molecular self-assembly and reorganization of the metal surface.« less

Self-assembly of acetate adsorbates drives atomic rearrangement on the Au(110) surface

PubMed Central

Hiebel, Fanny; Shong, Bonggeun; Chen, Wei; Madix, Robert J.; Kaxiras, Efthimios; Friend, Cynthia M.

2016-01-01

Weak inter-adsorbate interactions are shown to play a crucial role in determining surface structure, with major implications for its catalytic reactivity. This is exemplified here in the case of acetate bound to Au(110), where the small extra energy of the van der Waals interactions among the surface-bound groups drives massive restructuring of the underlying Au. Acetate is a key intermediate in electro-oxidation of CO2 and a poison in partial oxidation reactions. Metal atom migration originates at surface defects and is likely facilitated by weakened Au–Au interactions due to bonding with the acetate. Even though the acetate is a relatively small molecule, weak intermolecular interaction provides the energy required for molecular self-assembly and reorganization of the metal surface. PMID:27731407

Structure-directing weak phosphoryl XH...O=P (X = C, N) hydrogen bonds in cyclic oxazaphospholidines and oxazaphosphinanes.

PubMed

van der Lee, A; Rolland, M; Marat, X; Virieux, D; Volle, J N; Pirat, J L

2008-04-01

The structures of six cyclic oxazaphospholidines and three cyclic oxazaphosphinanes have been determined and their supramolecular structures have been compared. The molecules differ with respect to the functional groups attached to the central five- or six-membered rings, but have one phosphoryl group in common. The predominant feature in the supramolecular structures is the existence of relatively weak intermolecular phosphoryl XH...O=P (X = C, N) hydrogen bonds, creating in nearly all cases linear zigzag or double molecular chains. The molecular chains are in general linked to each other via very weak CH...pi or usual hydrogen-bond interactions. A survey of the Cambridge Structural Database on similar XH...O=P interactions shows a very large flexibility of the XH...O angle, which is in agreement with the DFT calculation reported elsewhere. The strength of the XH...O=P interaction can therefore be considered as relatively weak to moderately strong, and is expected to play at least a role in the formation of secondary substructures.

Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

NASA Astrophysics Data System (ADS)

Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

2018-04-01

The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

Weak competing interactions control assembly of strongly bonded TCNQ ionic acceptor molecules on silver surfaces

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

Park, Changwon; Rojas, Geoffrey A.; Jeon, Seokmin

2014-09-19

The energy scales of interactions that control molecular adsorption and assembly on surfaces can vary by several orders of magnitude, yet the importance of each contributing interaction is not apparent a priori. Tetracyanoquinodimethane (TCNQ) is an archetypal electron acceptor molecule and it is a key component of organic metals. On metal surfaces, this molecule also acts as an electron acceptor, producing negatively charged adsorbates. It is therefore rather intriguing to observe attractive molecular interactions in this system that were reported previously for copper and silver surfaces. In this paper, our experiments compared TCNQ adsorption on noble metal surfaces of Ag(100)more » and Ag(111). In both cases we found net attractive interactions down to the lowest coverage. However, the morphology of the assemblies was strikingly different, with two-dimensional islands on Ag(100) and one-dimensional chains on Ag(111) surfaces. This observation suggests that the registry effect governed by the molecular interaction with the underlying lattice potential is critical in determining the dimensionality of the molecular assembly. Using first-principles density functional calculations with a van der Waals correction scheme, we revealed that the strengths of major interactions (i.e., lattice potential corrugation, intermolecular attraction, and charge-transfer-induced repulsion) are all similar in energy. The van der Waals interactions, in particular, almost double the strength of attractive interactions, making the intermolecular potential comparable in strength to the diffusion potential and promoting self-assembly. However, it is the anisotropy of local intermolecular interactions that is primarily responsible for the difference in the topology of the molecular islands on Ag(100) and Ag(111) surfaces. Finally, we anticipate that the intermolecular potential will become more attractive and dominant over the diffusion potential with increasing molecular size, providing new design strategies for the structure and charge transfer within molecular layers.« less

Effects of strong hydrogen bonds and weak intermolecular interactions on supramolecular assemblies of 4-fluorobenzylamine

NASA Astrophysics Data System (ADS)

Wang, Shi; Ding, Xue-Hua; Li, Yong-Hua; Huang, Wei

2015-07-01

A series of supramolecular salts have been obtained by the self-assembly of 4-fluorobenzylamine and halide ions or metal chloride with 18-crown-6 as the host in the hydrochloric acid medium, i.e. (C7H9FN)+ṡX- (X = Cl-, 1; Br-, 2), [(C7H9FN)2ṡ(18-crown-6)2]2+ṡ(MCl4)2- (M = Mn, 3; Co, 5; Zn, 7; Cd, 8), [(C7H9FN)ṡ(18-crown-6)]+ṡ(FeCl4)- (4) and [(C7H9FN)ṡ(18-crown-6)]+ṡ1/2(CuCl4)2- (6). Structural analyses indicate that 1-2 crystallize in the triclinic space group P-1, 4 in orthorhombic space group Pnma and 3, 5, 6-8 in the monoclinic space group P21/c or C2/c. In these compounds, extensive intermolecular interactions have been utilized for the self-assembly of diverse supramolecular architectures, ranging from strong N-H⋯X (X = O, Cl, Br) hydrogen bonds to weak C-H⋯Y (Y = F, Cl, π) interactions. N-H⋯Cl/Br hydrogen bonds offer the major driving force in the crystal packing of salts 1-2 while N-H⋯O hydrogen bonds are found in salts 3-8.

Engineering On-Surface Spin Crossover: Spin-State Switching in a Self-Assembled Film of Vacuum-Sublimable Functional Molecule.

PubMed

Kumar, Kuppusamy Senthil; Studniarek, Michał; Heinrich, Benoît; Arabski, Jacek; Schmerber, Guy; Bowen, Martin; Boukari, Samy; Beaurepaire, Eric; Dreiser, Jan; Ruben, Mario

2018-03-01

The realization of spin-crossover (SCO)-based applications requires study of the spin-state switching characteristics of SCO complex molecules within nanostructured environments, especially on surfaces. Except for a very few cases, the SCO of a surface-bound thin molecular film is either quenched or heavily altered due to: (i) molecule-surface interactions and (ii) differing intermolecular interactions in films relative to the bulk. By fabricating SCO complexes on a weakly interacting surface, the interfacial quenching problem is tackled. However, engineering intermolecular interactions in thin SCO active films is rather difficult. Here, a molecular self-assembly strategy is proposed to fabricate thin spin-switchable surface-bound films with programmable intermolecular interactions. Molecular engineering of the parent complex system [Fe(H 2 B(pz) 2 ) 2 (bpy)] (pz = pyrazole, bpy = 2,2'-bipyridine) with a dodecyl (C 12 ) alkyl chain yields a classical amphiphile-like functional and vacuum-sublimable charge-neutral Fe II complex, [Fe(H 2 B(pz) 2 ) 2 (C 12 -bpy)] (C 12 -bpy = dodecyl[2,2'-bipyridine]-5-carboxylate). Both the bulk powder and 10 nm thin films sublimed onto either quartz glass or SiO x surfaces of the complex show comparable spin-state switching characteristics mediated by similar lamellar bilayer like self-assembly/molecular interactions. This unprecedented observation augurs well for the development of SCO-based applications, especially in molecular spintronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-dimensional six-connecting organic building blocks based on polychlorotriphenylmethyl units--synthesis, self-assembly, and magnetic properties.

PubMed

Roques, Nans; Maspoch, Daniel; Wurst, Klaus; Ruiz-Molina, Daniel; Rovira, Concepció; Veciana, Jaume

2006-12-13

The synthesis of a three-dimensional, six-connecting, organic building block based on a robust, rigid, and open-shell polychlorotriphenylmethyl (PTM) unit (radical 1) is reported, and its self-assembly properties are described in detail. The tendencies of this highly polar molecule and its hydrogenated precursor, compound 4, to form hydrogen bonds with oxygenated solvents ([1THF(6)] and [4THF(6)]) were reduced by replacing THF with diethyl ether in the crystallization process to yield two-dimensional (2D) hydrogen-bonded structures ([1(Et(2)O)(3)] and [4(Et(2)O)(3)]). The presence of direct hydrogen bonds between the radicals in the latter phase of 1 gives rise to very weak ferromagnetic intermolecular interactions at low temperatures, whereas when the radicals are isolated by THF molecules these interactions are antiferromagnetic and very weak. The role played by the carboxylic groups not only in the self-assembly properties but also in the transmission of the magnetic interactions has been illustrated by determination of the crystal structure and measurement of the magnetic properties of the corresponding hexaester radical 6, in which the close packing of molecular units gives rise to weak antiferromagnetic intermolecular interactions. Attempts to avoid solvation of the molecules in the solid state and to increase the structural and magnetic dimensionality were pursued by recrystallization of both compounds 1 and 4 from concentrated nitric acid, affording two three-dimensional (3D) robust hydrogen-bonded structures. While the structure obtained with compound 4 is characterized by the presence of polar channels and boxes containing water guest molecules along the c axis, radical 1 was oxidized to the corresponding fuchsone 10, which presented a completely different close-packed, guest-free structure.

4-Meth-oxy-3-(meth-oxy-meth-yl)benzalde-hyde.

PubMed

Zhang, Jing-Chao; Sun, Jun; Zhang, Juan; Liu, Guang-Lin; Guo, Cheng

2013-01-01

In the title compound, C10H12O3, the dihedral angle between the benzene ring and the meth-oxy-methyl side chain is 9.7 (2)°. The O atom of the aldehyde group and the C atom of the meth-oxy group deviate from the plane of the ring by 0.039 (3) and 0.338 (4) Å, respectively. The only inter-molecular inter-actions are very weak C-H⋯π inter-actions.

The intermolecular interaction in D2 - CX4 and O2 - CX4 (X = F, Cl) systems: Molecular beam scattering experiments as a sensitive probe of the selectivity of charge transfer component.

PubMed

Cappelletti, David; Falcinelli, Stefano; Pirani, Fernando

2016-10-07

Gas phase collisions of a D 2 projectile by CF 4 and by CCl 4 targets have been investigated with the molecular beam technique. The integral cross section, Q, has been measured for both collisional systems in the thermal energy range and oscillations due to the quantum "glory" interference have been resolved in the velocity dependence of Q. The analysis of the measured Q(v) data provided novel information on the anisotropic potential energy surfaces of the studied systems at intermediate and large separation distances. The relative role of the most relevant types of contributions to the global interaction has been characterized. Extending the phenomenology of a weak intermolecular halogen bond, the present work demonstrates that while D 2 - CF 4 is basically bound through the balance between size (Pauli) repulsion and dispersion attraction, an appreciable intermolecular bond stabilization by charge transfer is operative in D 2 - CCl 4 . We also demonstrated that the present analysis is consistent with that carried out for the F( 2 P)-D 2 and Cl( 2 P)-D 2 systems, previously characterized by scattering experiments performed with state-selected halogen atom beams. A detailed comparison of the present and previous results on O 2 -CF 4 and O 2 -CCl 4 systems pinpointed striking differences in the behavior of hydrogen and oxygen molecules when they interact with the same partner, mainly due to the selectivity of the charge transfer component. The present work contributes to cast light on the nature and role of the intermolecular interaction in prototype systems, involving homo-nuclear diatoms and symmetric halogenated molecules.

Substituent effects on the electronic characteristics of pentacene derivatives for organic electronic devices: dioxolane-substituted pentacene derivatives with triisopropylsilylethynyl functional groups.

PubMed

Griffith, Olga Lobanova; Anthony, John E; Jones, Adolphus G; Shu, Ying; Lichtenberger, Dennis L

2012-08-29

The intramolecular electronic structures and intermolecular electronic interactions of 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS pentacene), 6,14-bis-(triisopropylsilylethynyl)-1,3,9,11-tetraoxa-dicyclopenta[b,m]-pentacene (TP-5 pentacene), and 2,2,10,10-tetraethyl-6,14-bis-(triisopropylsilylethynyl)-1,3,9,11-tetraoxa-dicyclopenta[b,m]pentacene (EtTP-5 pentacene) have been investigated by the combination of gas-phase and solid-phase photoelectron spectroscopy measurements. Further insight has been provided by electrochemical measurements in solution, and the principles that emerge are supported by electronic structure calculations. The measurements show that the energies of electron transfer such as the reorganization energies, ionization energies, charge-injection barriers, polarization energies, and HOMO-LUMO energy gaps are strongly dependent on the particular functionalization of the pentacene core. The ionization energy trends as a function of the substitution observed for molecules in the gas phase are not reproduced in measurements of the molecules in the condensed phase due to polarization effects in the solid. The electronic behavior of these materials is impacted less by the direct substituent electronic effects on the individual molecules than by the indirect consequences of substituent effects on the intermolecular interactions. The ionization energies as a function of film thickness give information on the relative electrical conductivity of the films, and all three molecules show different material behavior. The stronger intermolecular interactions in TP-5 pentacene films lead to better charge transfer properties versus those in TIPS pentacene films, and EtTP-5 pentacene films have very weak intermolecular interactions and the poorest charge transfer properties of these molecules.

Interaction between Al3+ and acrylic acid and polyacrylic acid in acidic aqueous solution: a model experiment for the behavior of Al3+ in acidified soil solution.

PubMed

Etou, Mayumi; Masaki, Yuka; Tsuji, Yutaka; Saito, Tomoyuki; Bai, Shuqin; Nishida, Ikuko; Okaue, Yoshihiro; Yokoyama, Takushi

2011-01-01

From the viewpoint of the phytotoxicity and mobility of Al(3+) released from soil minerals due to soil acidification, the interaction between Al(3+) and acrylic acid (AA) and polyacrylic acid (PAA) as a model compound of fulvic acid was investigated. The interaction was examined at pH 3 so as to avoid the hydrolysis of Al(3+). The interaction between Al(3+) and AA was weak. However, the interaction between Al(3+) and PAA was strong and depended on the initial (COOH in PAA)/Al molar ratio (R(P)) of the solution. For the range of 1/R(P), the interaction between Al(3+) and PAA can be divided into three categories: (1) 1:1 Al-PAA-complex (an Al(3+) combines to a carboxyl group), (2) intermolecular Al-PAA-complex (an Al(3+) combines to more than 2 carboxyl groups of other Al-PAA-complexes) in addition to the 1:1 Al-PAA-complex and (3) precipitation of intermolecular complexes. In conclusion, R(P) is an important factor affecting the behavior of Al(3+) in acidic soil solution.

Supramolecular assembly of group 11 phosphorescent metal complexes for chemosensors of alcohol derivatives

NASA Astrophysics Data System (ADS)

Lintang, H. O.; Ghazalli, N. F.; Yuliati, L.

2018-04-01

We report on systematic study on vapochromic sensing of ethanol by using phosphorescent trinuclear metal pyrazolate complexes with supramolecular assembly of weak intermolecular metal-metal interactions using 4-(3,5-dimethoxybenzyl)-3,5-dimethyl pyrazole ligand (1) and group 11 metal ions (Cu(I), Ag(I), Au(I)). Upon excitation at 284, the resulting complexes showed emission bands with a peak centered at 616, 473 and 612 nm for 2(Cu), 2(Ag) and 2(Au), respectively. Chemosensor 2(Cu) showed positive response to ethanol vapors in 5 mins by blue-shifting its emission band from 616 to 555 nm and emitting bright orange to green. Otherwise 2(Au) gave shifting from its emission band centered at 612 to 587 nm with Δλ of 25 nm (41%) and color changes from red-orange to light green-orange while 2(Ag) showed quenching in its original emission intensity at 473 nm in 40% with color changes from dark green to less emissive. These results demonstrate that sensing capability of chemosensor 2(Cu) with suitable molecular design of ligand and metal ion in the complex is due to the formation of a weak intermolecular hydrogen bonding interaction of O atom at the methoxy of the benzyl ring with the OH of the vapors at the outside of the molecules.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.

PubMed

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I; Blackledge, Martin; van Nuland, Nico A J

2009-05-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 muM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (K(d) = 132 +/- 13 muM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein-protein complexes.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex

PubMed Central

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I.; Blackledge, Martin; van Nuland, Nico A. J.

2009-01-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 μM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (Kd = 132 ± 13 μM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein–protein complexes. PMID:19359362

Synthesis, structure, computational and in-silico anticancer studies of N,N-diethyl-N‧-palmitoylthiourea

NASA Astrophysics Data System (ADS)

Asegbeloyin, Jonnie Niyi; Oyeka, Ebube Evaristus; Okpareke, Obinna; Ibezim, Akachukwu

2018-02-01

A new potential ONS donor ligand N,N-diethyl-N‧-palmitoylthiourea (PACDEA) with the molecular formular C21H42N2OS has been synthesized and characterized by ESI-MS, UV, FTIR 1H and 13C NMR spectroscopy and single X-ray crystallography. The asymmetric molecules crystallized in the centrosymmetric structure of monoclinic crystal system with space group P21/c. In the crystal structure of the compound, molecules are linked in a continuous chain by intermolecular Nsbnd H⋯Odbnd C hydrogen bonds, which stabilized the crystal structure. The palmitoyl moiety and N (2)-ethyl group lie on a plane, while the thiocarbonyl moiety is twisted and lying othorgonal to the plane. Non-covalent interaction (NCI) analysis on the hydrogen bonded solid state structure of the molecule revealed the presence of a significant number of non-covalent interactions including intermolecular hydrogen bonding interactions, Csbnd Hsbnd -lone pair interactions, weak Van der Waals interactions, and steric/ring closure interactions. The NCI analysis also showed the presence of intramolecular stabilizing Csbnd H⋯Odbnd C and Csbnd H⋯Sdbnd C interactions. Docking simulation revealed that the compound interacted favourably with ten selected validated anticancer drug targets, which is an indication that the compound could possess some anticancer properties.

Molecular Motions in Functional Self-Assembled Nanostructures

PubMed Central

Dhotel, Alexandre; Chen, Ziguang; Delbreilh, Laurent; Youssef, Boulos; Saiter, Jean-Marc; Tan, Li

2013-01-01

The construction of “smart” materials able to perform specific functions at the molecular scale through the application of various stimuli is highly attractive but still challenging. The most recent applications indicate that the outstanding flexibility of self-assembled architectures can be employed as a powerful tool for the development of innovative molecular devices, functional surfaces and smart nanomaterials. Structural flexibility of these materials is known to be conferred by weak intermolecular forces involved in self-assembly strategies. However, some fundamental mechanisms responsible for conformational lability remain unexplored. Furthermore, the role played by stronger bonds, such as coordination, ionic and covalent bonding, is sometimes neglected while they can be employed readily to produce mechanically robust but also chemically reversible structures. In this review, recent applications of structural flexibility and molecular motions in self-assembled nanostructures are discussed. Special focus is given to advanced materials exhibiting significant performance changes after an external stimulus is applied, such as light exposure, pH variation, heat treatment or electromagnetic field. The crucial role played by strong intra- and weak intermolecular interactions on structural lability and responsiveness is highlighted. PMID:23348927

Exploring the structural changes on excitation of a luminescent organic bromine-substituted complex by in-house time-resolved pump-probe diffraction

DOE PAGES

Basuroy, Krishnayan; Chen, Yang; Sarkar, Sounak; ...

2017-03-09

The structural changes accompanying the excitation of the luminescent dibromobenzene derivative, 1,4-dibromo-2,5-bis(octyloxy)benzene, have been measured by in-house monochromatic time-resolved (TR) diffraction at 90 K. Results show an increment of the very short intermolecular Br•••Br contact distance from 3.290 Å to 3.380 Å. These calculations show the Br…Br interaction to be strongly repulsive in both the Ground and Excited states but significantly relaxed by the lengthening of the contact distance on excitation. The stability of the crystals is attributed to the many weak C-H···Br and C-H···π intermolecular interactions. Our study described is the first practical application of In-House Time-Resolved diffraction, mademore » possible by the continuing increase in the brightness of X-ray sources and the sensitivity of our detectors.« less

Exploring the structural changes on excitation of a luminescent organic bromine-substituted complex by in-house time-resolved pump-probe diffraction

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

Basuroy, Krishnayan; Chen, Yang; Sarkar, Sounak

The structural changes accompanying the excitation of the luminescent dibromobenzene derivative, 1,4-dibromo-2,5-bis(octyloxy)benzene, have been measured by in-house monochromatic time-resolved (TR) diffraction at 90 K. Results show an increment of the very short intermolecular Br•••Br contact distance from 3.290 Å to 3.380 Å. These calculations show the Br…Br interaction to be strongly repulsive in both the Ground and Excited states but significantly relaxed by the lengthening of the contact distance on excitation. The stability of the crystals is attributed to the many weak C-H···Br and C-H···π intermolecular interactions. Our study described is the first practical application of In-House Time-Resolved diffraction, mademore » possible by the continuing increase in the brightness of X-ray sources and the sensitivity of our detectors.« less

Spectroscopic detection of halogen bonding resolves dye regeneration in the dye-sensitized solar cell.

PubMed

Parlane, Fraser G L; Mustoe, Chantal; Kellett, Cameron W; Simon, Sarah J; Swords, Wesley B; Meyer, Gerald J; Kennepohl, Pierre; Berlinguette, Curtis P

2017-11-24

The interactions between a surface-adsorbed dye and a soluble redox-active electrolyte species in the dye-sensitized solar cell has a significant impact on the rate of regeneration of photo-oxidized dye molecules and open-circuit voltage of the device. Dyes must therefore be designed to encourage these interfacial interactions, but experimentally resolving how such weak interactions affect electron transfer is challenging. Herein, we use X-ray absorption spectroscopy to confirm halogen bonding can exist at the dye-electrolyte interface. Using a known series of triphenylamine-based dyes bearing halogen substituents geometrically positioned for reaction with halides in solution, halogen bonding was detected only in cases where brominated and iodinated dyes were photo-oxidized. This result implies that weak intermolecular interactions between photo-oxidized dyes and the electrolyte can impact device photovoltages. This result was unexpected considering the low concentration of oxidized dyes (less than 1 in 100,000) under full solar illumination.

Unraveling orbital hybridization of triplet emitters at the metal-organic interface.

PubMed

Ewen, Pascal R; Sanning, Jan; Doltsinis, Nikos L; Mauro, Matteo; Strassert, Cristian A; Wegner, Daniel

2013-12-27

We have investigated the structural and electronic properties of phosphorescent planar platinum(II) complexes at the interface of Au(111) with submolecular resolution using combined scanning tunneling microscopy and spectroscopy as well as density functional theory. Our analysis shows that molecule-substrate coupling and lateral intermolecular interactions are weak. While the ligand orbitals remain essentially unchanged upon contact with the substrate, we found modified electronic behavior at the Pt atom due to local hybridization and charge transfer to the substrate. Thus, this novel class of phosphorescent molecules exhibits well-defined and tunable interaction with its local environment.

Methyl 4-eth-oxy-2-methyl-2H-1,2-benzothia-zine-3-carboxyl-ate 1,1-dioxide.

PubMed

Zia-Ur-Rehman, Muhammad; Choudary, Jamil Anwar; Elsegood, Mark R J; Akbar, Noshin; Latif Siddiqui, Hamid

2008-07-16

In the crystal structure of the title compound, C(13)H(15)NO(5)S, the mol-ecules exhibit weak S=O⋯H-C and C=O⋯H-C inter-molecular inter-actions and arrange themselves into centrosymmetric dimers by means of π-π inter-actions (ring centroids are separated by 3.619 Å, while the closest C⋯C contacts are 3.514 Å). 1,2-Benzothia-zines of this kind have a range of biological activities and are used as medicines in the treatment of inflammation and rheumatoid arthritis.

Eight supramolecular assemblies constructed from bis(benzimidazole) and organic acids through strong classical hydrogen bonding and weak noncovalent interactions

NASA Astrophysics Data System (ADS)

Jin, Shouwen; Wang, Daqi

2014-05-01

Eight crystalline organic acid-base adducts derived from alkane bridged bis(N-benzimidazole) and organic acids (2,4,6-trinitrophenol, p-nitrobenzoic acid, m-nitrobenzoic acid, 3,5-dinitrobenzoic acid, 5-sulfosalicylic acid and oxalic acid) were prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. Of the eight compounds five are organic salts (1, 4, 6, 7 and 8) and the other three (2, 3, and 5) are cocrystals. In all of the adducts except 1 and 8, the ratio of the acid and the base is 2:1. All eight supramolecular assemblies involve extensive intermolecular classical hydrogen bonds as well as other noncovalent interactions. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, all the complexes displayed 3D framework structure. The results presented herein indicate that the strength and directionality of the classical N+-H⋯O-, O-H⋯O, and O-H⋯N hydrogen bonds (ionic or neutral) and other nonbonding associations between acids and ditopic benzimidazoles are sufficient to bring about the formation of cocrystals or organic salts.

Aqua-(3-fluoro-benzoato-κO)(3-fluoro-benzoato-κO,O')(1,10-phenanthroline-κN,N')cobalt(II).

PubMed

Wang, Xiao-Hui; Sun, Li-Mei

2012-01-01

In the title compound, [Co(C(7)H(4)FO(2))(2)(C(12)H(8)N(2))(H(2)O)], the Co(II) ion is coordinated by two O atoms from one 3-fluoro-benzoate (fb) ligand and one O atom from another fb ligand, two N atoms from the 1,10-phenanthroline ligand and a water mol-ecule in a distorted octa-hedral geometry. An intra-molecular O-H⋯O hydrogen bond occurs. Inter-molecular O-H⋯O hydrogen bonds link pairs of mol-ecules into centrosymmetric dimers. Weak inter-molecular C-H⋯O and C-H⋯F hydrogen bonds and π-π inter-actions between the aromatic rings [shortest centroid-centroid distance = 3.4962 (2) Å] further stabilize the crystal packing.

Structural and computational analysis of intermolecular interactions in a new 2-thiouracil polymorph.

PubMed

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Sanković, Krešimir

2017-12-01

The crystallization and characterization of a new polymorph of 2-thiouracil by single-crystal X-ray diffraction, Hirshfeld surface analysis and periodic density functional theory (DFT) calculations are described. The previously published polymorph (A) crystallizes in the triclinic space group P\\overline{1}, while that described herein (B) crystallizes in the monoclinic space group P2 1 /c. Periodic DFT calculations showed that the energies of polymorphs A and B, compared to the gas-phase geometry, were -108.8 and -29.4 kJ mol -1 , respectively. The two polymorphs have different intermolecular contacts that were analyzed and are discussed in detail. Significant differences in the molecular structure were found only in the bond lengths and angles involving heteroatoms that are involved in hydrogen bonds. Decomposition of the Hirshfeld fingerprint plots revealed that O...H and S...H contacts cover over 50% of the noncovalent contacts in both of the polymorphs; however, they are quite different in strength. Hydrogen bonds of the N-H...O and N-H...S types were found in polymorph A, whereas in polymorph B, only those of the N-H...O type are present, resulting in a different packing in the unit cell. QTAIM (quantum theory of atoms in molecules) computational analysis showed that the interaction energies for these weak-to-medium strength hydrogen bonds with a noncovalent or mixed interaction character were estimated to fall within the ranges 5.4-10.2 and 4.9-9.2 kJ mol -1 for polymorphs A and B, respectively. Also, the NCI (noncovalent interaction) plots revealed weak stacking interactions. The interaction energies for these interactions were in the ranges 3.5-4.1 and 3.1-5.5 kJ mol -1 for polymorphs A and B, respectively, as shown by QTAIM analysis.

4-[(1E)-3-(2,6-Dichloro-3-fluoro-phen-yl)-3-oxoprop-1-en-1-yl]benzonitrile.

PubMed

Praveen, Aletti S; Yathirajan, Hemmige S; Narayana, Badiadka; Gerber, Thomas; Hosten, Eric; Betz, Richard

2012-05-01

In the title mol-ecule, C(16)H(8)Cl(2)FNO, the benzene rings form a dihedral angle of 78.69 (8)°. The F atom is disordered over two positions in a 0.530 (3):0.470 (3) ratio. The crystal packing exhibits π-π inter-actions between dichloro-substituted rings [centroid-centroid distance = 3.6671 (10) Å] and weak inter-molecular C-H⋯F contacts.

Molecular association via halogen bonding and other weak interactions in the crystal structures of 11-bromo-12-oxo-5β-cholan derivatives

NASA Astrophysics Data System (ADS)

Salunke, Deepak B.; Hazra, Braja G.; Gonnade, Rajesh G.; Pore, Vandana S.; Bhadbhade, Mohan M.

2008-12-01

Methyl 3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 2, methyl 11α-bromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 3, methyl 11β-bromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 4 and methyl 11,11-dibromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 5 were synthesized. The crystal structures of these molecules were resolved to study the effect of bulky bromine atom in the steroid skeleton of cholic acid with different stereo-chemical orientations at C-11 on the two-dimensional arrangement of molecules and solid-state properties. All the molecules associate only via weak intermolecular interactions in their crystal structures, notable one being the Halogen Bonded assembly (C-Br…O) in 5.

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

Mikhlina, Ya. A., E-mail: altik@inbox.ru; Bolotin, B. M.; Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru

Two crystal modifications (1o and 1y) of N-butyl-2-cyano-3-[4-(dimethylamino)phenyl]-2-propenamide, which differ in the color of crystals and the color of luminescence, have been studied by X-ray diffraction and spectral-luminescence methods. The corresponding bond lengths and bond angles in the molecules of two crystal modifications are virtually identical. In both crystal structures, there are two systems of weak intermolecular interactions: {pi}-stacking interactions and -CN Horizontal-Ellipsis H-N hydrogen bonds involving nitrile and NH groups. In the crystal structures, two hydrogen bonds connect pairs of molecules into centrosymmetric dimers. The N Horizontal-Ellipsis H distances are 2.21 and 2.41 A in 1o and 1y, respectively.more » The interplanar distances in the {pi}-stacked systems of 1o and 1y are 3.33 and 3.41 A, respectively. Both types of weak interactions are stronger in 1o than in 1y, which accounts for a larger shift of absorption and luminescence bands for the former compound.« less

Ab initio study of the CO-N2 complex: a new highly accurate intermolecular potential energy surface and rovibrational spectrum.

PubMed

Cybulski, Hubert; Henriksen, Christian; Dawes, Richard; Wang, Xiao-Gang; Bora, Neha; Avila, Gustavo; Carrington, Tucker; Fernández, Berta

2018-05-09

A new, highly accurate ab initio ground-state intermolecular potential-energy surface (IPES) for the CO-N2 complex is presented. Thousands of interaction energies calculated with the CCSD(T) method and Dunning's aug-cc-pVQZ basis set extended with midbond functions were fitted to an analytical function. The global minimum of the potential is characterized by an almost T-shaped structure and has an energy of -118.2 cm-1. The symmetry-adapted Lanczos algorithm was used to compute rovibrational energies (up to J = 20) on the new IPES. The RMSE with respect to experiment was found to be on the order of 0.038 cm-1 which confirms the very high accuracy of the potential. This level of agreement is among the best reported in the literature for weakly bound systems and considerably improves on those of previously published potentials.

Geminal-spanning orbitals make explicitly correlated reduced-scaling coupled-cluster methods robust, yet simple

NASA Astrophysics Data System (ADS)

Pavošević, Fabijan; Neese, Frank; Valeev, Edward F.

2014-08-01

We present a production implementation of reduced-scaling explicitly correlated (F12) coupled-cluster singles and doubles (CCSD) method based on pair-natural orbitals (PNOs). A key feature is the reformulation of the explicitly correlated terms using geminal-spanning orbitals that greatly reduce the truncation errors of the F12 contribution. For the standard S66 benchmark of weak intermolecular interactions, the cc-pVDZ-F12 PNO CCSD F12 interaction energies reproduce the complete basis set CCSD limit with mean absolute error <0.1 kcal/mol, and at a greatly reduced cost compared to the conventional CCSD F12.

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities.

PubMed

Lovelock, Kevin R J

2017-12-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced , is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, ced IP , where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, ced C+A , where the ionic vapour constituents are isolated ions. A ced IP dataset is presented for 64 ILs. For the first time an experimental ced C+A , a measure of the strength of the total intermolecular interaction for an IL, is presented. ced C+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between ced IP and the inverse of the molecular volume. A good linear correlation is found between IL ced IP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to ced IP . These findings show that ced IP is very important for understanding IL intermolecular interactions, in spite of ced IP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined.

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities

PubMed Central

2017-01-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced, is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, cedIP, where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, cedC+A, where the ionic vapour constituents are isolated ions. A cedIP dataset is presented for 64 ILs. For the first time an experimental cedC+A, a measure of the strength of the total intermolecular interaction for an IL, is presented. cedC+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between cedIP and the inverse of the molecular volume. A good linear correlation is found between IL cedIP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to cedIP. These findings show that cedIP is very important for understanding IL intermolecular interactions, in spite of cedIP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined. PMID:29308254

An isotopic mass effect on the intermolecular potential

DOE PAGES

Herman, Michael F.; Currier, Robert Patrick; Clegg, Samuel M.

2015-09-28

The impact of isotopic variation on the electronic energy and intermolecular potentials is often suppressed when calculating isotopologue thermodynamics. Intramolecular potential energy surfaces for distinct isotopologues are in fact equivalent under the Born–Oppenheimer approximation, which is sometimes used to imply that the intermolecular interactions are independent of isotopic mass. In this paper, the intermolecular dipole–dipole interaction between hetero-nuclear diatomic molecules is considered. It is shown that the intermolecular potential contains mass-dependent terms even though each nucleus moves on a Born–Oppenheimer surface. Finally, the analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologuemore » thermodynamics.« less

Intermolecular configurations dominated by quadrupole-quadrupole electrostatic interactions: explicit correlation treatment of the five-dimensional potential energy surface and infrared spectra for the CO-N2 complex.

PubMed

Liu, Jing-Min; Zhai, Yu; Zhang, Xiao-Long; Li, Hui

2018-01-17

A thorough understanding of the intermolecular configurations of van der Waals complexes is a great challenge due to their weak interactions, floppiness and anharmonic nature. Although high-resolution microwave or infrared spectroscopy provides one of the most direct and precise pieces of experimental evidence, the origin and key role in determining such intermolecular configurations of a van der Waals system strongly depend on its highly accurate potential energy surface (PES) and a detailed analysis of its ro-vibrational wavefunctions. Here, a new five-dimensional potential energy surface for the van der Waals complex of CO-N 2 which explicitly incorporates the dependence on the stretch coordinate of the CO monomer is generated using the explicitly correlated couple cluster (CCSD(T)-F12) method in conjunction with a large basis set. Analytic four-dimensional PESs are obtained by the least-squares fitting of vibrationally averaged interaction energies for v = 0 and v = 1 to the Morse/Long-Range potential mode (V MLR ). These fits to 7966 points have root-mean-square deviations (RMSD) of 0.131 cm -1 and 0.129 cm -1 for v = 0 and v = 1, respectively, with only 315 parameters. Energy decomposition analysis is carried out, and it reveals that the dominant factor in controlling intermolecular configurations is quadrupole-quadrupole electrostatic interactions. Moreover, the rovibrational levels and wave functions are obtained for the first time. The predicted infrared transitions and intensities for the ortho-N 2 -CO complex as well as the calculated energy levels for para-N 2 -CO are in good agreement with the available experimental data with RMSD discrepancies smaller than 0.068 cm -1 . The calculated infrared band origin shift associated with the fundamental band frequency of CO is -0.721 cm -1 for ortho-N 2 -CO which is in excellent agreement with the experimental value of -0.739 cm -1 . The agreement with experimental values validates the high quality of the PESs and enhances our confidence to explain the observed mystery lines around 2163 cm -1 .

Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases

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

Bartocci, Alessio; Cappelletti, David; Pirani, Fernando

2015-05-14

The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl{sub 4} and CF{sub 4}. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypicalmore » Ng-CCl{sub 4} and Ng-CF{sub 4} and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF{sub 4}, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl{sub 4}, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential suggested by the analysis of the experiments actually reflect two chemically meaningful contributions, namely, a stabilizing interaction arising from the anisotropy of the charge distribution around the Cl atom in CCl{sub 4} and a stereospecific electron transfer that occurs at the intermolecular distances mainly probed by the experiments. Our model calculations suggest that the largest effect is for the vertex geometry of CCl{sub 4} while other geometries appear to play a minor to negligible role.« less

Weak Interactions Govern the Viscosity of Concentrated Antibody Solutions: High-Throughput Analysis Using the Diffusion Interaction Parameter

PubMed Central

Connolly, Brian D.; Petry, Chris; Yadav, Sandeep; Demeule, Barthélemy; Ciaccio, Natalie; Moore, Jamie M.R.; Shire, Steven J.; Gokarn, Yatin R.

2012-01-01

Weak protein-protein interactions are thought to modulate the viscoelastic properties of concentrated antibody solutions. Predicting the viscoelastic behavior of concentrated antibodies from their dilute solution behavior is of significant interest and remains a challenge. Here, we show that the diffusion interaction parameter (kD), a component of the osmotic second virial coefficient (B2) that is amenable to high-throughput measurement in dilute solutions, correlates well with the viscosity of concentrated monoclonal antibody (mAb) solutions. We measured the kD of 29 different mAbs (IgG1 and IgG4) in four different solvent conditions (low and high ion normality) and found a linear dependence between kD and the exponential coefficient that describes the viscosity concentration profiles (|R| ≥ 0.9). Through experimentally measured effective charge measurements, under low ion normality where the electroviscous effect can dominate, we show that the mAb solution viscosity is poorly correlated with the mAb net charge (|R| ≤ 0.6). With this large data set, our results provide compelling evidence in support of weak intermolecular interactions, in contrast to the notion that the electroviscous effect is important in governing the viscoelastic behavior of concentrated mAb solutions. Our approach is particularly applicable as a screening tool for selecting mAbs with desirable viscosity properties early during lead candidate selection. PMID:22828333

A chiral aluminum solvating agent (CASA) for 1H NMR chiral analysis of alcohols at low temperature.

PubMed

Seo, Min-Seob; Jang, Sumin; Kim, Hyunwoo

2018-03-16

A chiral aluminum solvating agent (CASA) was demonstrated to be a general and efficient reagent for 1H NMR chiral analysis of alcohols. The sodium salt of the CASA (CASA-Na) showed a complete baseline peak separation of the hydroxyl group for various chiral alcohols including primary, secondary, and tertiary alcohols with alkyl and aryl substituents in CD3CN. Due to the weak intermolecular interaction, 1H NMR measurement at low temperature (-40 to 10 °C) was required.

Crystal structure of fenclorim.

PubMed

Kwon, Eunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

2015-10-01

In the title compound, C10H6Cl2N2 (systematic name: 4,6-di-chloro-2-phenyl-pyrimidine), which is used commercially as the herbicide safener, fenclorim, the dihedral angle between the di-chloro-pyrimidyl and phenyl rings is 9.45 (10)°. In the crystal, C-H⋯N hydrogen bonds link adjacent mol-ecules, forming chains along the c-axis direction. In addition, weak inter-molecular C-Cl⋯π [3.6185 (10) Å] and π-π [3.8796 (11) Å] inter-actions are present, forming a three-dimensional network.

Crystal structures of (2E)-1-(3-bromo-thio-phen-2-yl)-3-(2-meth-oxy-phen-yl)prop-2-en-1-one and (2E)-1-(3-bromo-thio-phen-2-yl)-3-(3,4-di-meth-oxy-phen-yl)prop-2-en-1-one.

PubMed

Naik, Vasant S; Shettigar, Venkataraya; Berglin, Tyler S; Coburn, Jillian S; Jasinski, Jerry P; Yathirajan, Hemmige S

2015-08-01

In the mol-ecules of the title compounds, (2E)-1-(3-bromo-thio-phen-2-yl)-3-(2-meth-oxy-phen-yl)prop-2-en-1-one, C14H11BrO2S, (I), which crystallizes in the space group P-1 with four independent mol-ecules in the asymmetric unit (Z' = 8), and (2E)-1-(3-bromo-thio-phen-2-yl)-3-(3,4-di-meth-oxy-phen-yl)prop-2-en-1-one, C15H13BrO3S, (II), which crystallizes with Z' = 8 in the space group I2/a, the non-H atoms are nearly coplanar. The mol-ecules of (I) pack with inversion symmetry stacked diagonally along the a-axis direction. Weak C-H⋯Br intra-molecular inter-actions in each of the four mol-ecules in the asymmetric unit are observed. In (II), weak C-H⋯O, bifurcated three-center inter-molecular inter-actions forming dimers along with weak C-H⋯π and π-π stacking inter-actions are observed, linking the mol-ecules into sheets along [001]. A weak C-H⋯Br intra-molecular inter-action is also present. There are no classical hydrogen bonds present in either structure.

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

Herman, Michael F.; Currier, Robert Patrick; Clegg, Samuel M.

The impact of isotopic variation on the electronic energy and intermolecular potentials is often suppressed when calculating isotopologue thermodynamics. Intramolecular potential energy surfaces for distinct isotopologues are in fact equivalent under the Born–Oppenheimer approximation, which is sometimes used to imply that the intermolecular interactions are independent of isotopic mass. In this paper, the intermolecular dipole–dipole interaction between hetero-nuclear diatomic molecules is considered. It is shown that the intermolecular potential contains mass-dependent terms even though each nucleus moves on a Born–Oppenheimer surface. Finally, the analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologuemore » thermodynamics.« less

Molecular Self-Assembly of Group 11 Pyrazolate Complexes as Phosphorescent Chemosensors for Detection of Benzene

NASA Astrophysics Data System (ADS)

Ghazalli, N. F.; Yuliati, L.; Lintang, H. O.

2018-01-01

We highlight the systematic study on vapochromic sensing of aromatic vapors such as benzene using phosphorescent trinuclear pyrazolate complexes (2) with supramolecular assembly of a weak intermolecular metal-metal interaction consisting of 4-(3,5-dimethoxybenzyl)-3,5-dimethyl pyrazole ligand (1) and group 11 metal ions (Cu(I), Ag(I), Au(I)). The resulting chemosensor 2(Cu) revealed positive response to benzene vapors in 5 mins by blue-shifting its emission band in 44 nm (from 616 to 572 nm) and emitted bright orange to green, where this change cannot be recovered even with external stimuli. Comparing to 2(Ag) with longer metal-metal distance (473 nm) with same sensing time and quenching in 37%, 2(Au) gave quenching in 81% from its original intensity at 612 nm with reusability in 82% without external stimuli and emitted less emissive of red-orange from its original color. The shifting phenomenon in 2(Cu) suggests diffusion of benzene vapors to inside molecules for formation of intermolecular interaction with Cu(I)-Cu(I) interaction while quenching phenomenon in 2(Au) suggests diffusion of benzene vapors to between the Au(I)-Au(I) interaction. These results indicate that suitable molecular structure of ligand and metal ion in pyrazolate complex is important for designing chemosensor in the detection of benzene vapors.

Low-frequency collective dynamics in deep eutectic solvents of acetamide and electrolytes: a femtosecond Raman-induced Kerr effect spectroscopic study.

PubMed

Biswas, Ranjit; Das, Anuradha; Shirota, Hideaki

2014-10-07

In this study, we have investigated the ion concentration dependent collective dynamics in two series of deep eutectic solvent (DES) systems by femtosecond Raman-induced Kerr effect spectroscopy, as well as some physical properties, e.g., shear viscosity (η), density (ρ), and surface tension (γ). The DES systems studied here are [0.75CH3CONH2 + 0.25{f KSCN + (1 - f )NaSCN}] and [0.78CH3CONH2 + 0.22{f LiBr + (1 - f )LiNO3}] with f = 0, 0.2, 0.4, 0.6, 0.8, and 1.0. γ of these DES systems shows near insensitivity to f, while ρ shows a moderate dependence on f. Interestingly, η exhibits a strong dependence on f. In the low-frequency Kerr spectra, obtained via the Fourier transform of the collected Kerr transients, a characteristic band at ∼70 cm(-1) is clear in [0.78CH3CONH2 + 0.22{f LiBr + (1 - f )LiNO3}] DES especially at the larger f. The band is attributed to the intermolecular hydrogen bond of acetamide. Because of less depolarized Raman activities of intermolecular/interionic vibrational motions, which are mostly translational (collision-induced or interaction-induced) motions, of spherical ions, the intermolecular hydrogen-bonding band is clearly observed. In contrast, the intermolecular hydrogen-bonding band is buried in the other intermolecular/interionic vibrational motions, which includes translational and reorientational (librational) motions and their cross-terms, in [0.75CH3CONH2 + 0.25{f KSCN + (1 - f )NaSCN}] system. The first moment (M1) of the intermolecular/interionic vibrational band in these DES systems is much higher than that in typical neutral molecular liquids and shows a weak but contrasting dependence on the bulk parameter √γ/ρ. The time constants for picosecond overdamped Kerr transients in both the DES systems, which are obtained on the basis of the analysis fitted by a triexponential function, are rather insensitive to f for both the DES systems, but all the three time constants (fast: ∼1-3 ps; intermediate: ∼7-20 ps; and slow: ∼100 ps) are different between the [0.78CH3CONH2 + 0.22{f LiBr + (1 - f )LiNO3}] and [0.75CH3CONH2 + 0.25{f KSCN + (1 - f )NaSCN}] systems. These results indicate that the intermolecular/interionic interactions in DES systems is strongly influenced by the ionic species present in these DES systems.

H2O-CH4 and H2S-CH4 complexes: a direct comparison through molecular beam experiments and ab initio calculations.

PubMed

Cappelletti, David; Bartocci, Alessio; Frati, Federica; Roncaratti, Luiz F; Belpassi, Leonardo; Tarantelli, Francesco; Lakshmi, Prabha Aiswarya; Arunan, Elangannan; Pirani, Fernando

2015-11-11

New molecular beam scattering experiments have been performed to measure the total (elastic plus inelastic) cross sections as a function of the velocity in collisions between water and hydrogen sulfide projectile molecules and the methane target. Measured data have been exploited to characterize the range and strength of the intermolecular interaction in such systems, which are of relevance as they drive the gas phase molecular dynamics and the clathrate formation. Complementary information has been obtained by rotational spectra, recorded for the hydrogen sulfide-methane complex, with a pulsed nozzle Fourier transform microwave spectrometer. Extensive ab initio calculations have been performed to rationalize all the experimental findings. The combination of experimental and theoretical information has established the ground for the understanding of the nature of the interaction and allows for its basic components to be modelled, including charge transfer, in these weakly bound systems. The intermolecular potential for H2S-CH4 is significantly less anisotropic than for H2O-CH4, although both of them have potential minima that can be characterized as 'hydrogen bonded'.

From dipolar to multipolar interactions between ultracold Feshbach molecules

NASA Astrophysics Data System (ADS)

Quéméner, Goulven; Lepers, Maxence; Luc-Koenig, Eliane; Dulieu, Olivier

2016-05-01

Using the multipolar expansion of electrostatic and magnetostatic potential energies, we characterize the long-range interactions between two weakly-bound diatomic molecules, taking as an example the paramagnetic Er2 Feshbach molecules which were produced recently. The interaction between atomic magnetic dipoles gives rise to the usual R-3 leading term of the multipolar expansion, where R is the intermolecular distance. We show that additional terms scaling as R-5, R-7 and so on also appear, which are strongly anisotropic with respect to the orientation of the molecules. These terms can be seen as effective molecular multipole moments reflecting the spatial extension of the molecules which is non-negligible compared to R. We acknowledge the financial support of the COPOMOL project (ANR-13-IS04-0004) from Agence Nationale de la Recherche.

Intermolecular orbital interaction in π systems

NASA Astrophysics Data System (ADS)

Zhao, Rundong; Zhang, Rui-Qin

2018-04-01

Intermolecular interactions, in regard to which people tend to emphasise the noncovalent van der Waals (vdW) forces when conducting investigations throughout chemistry, can influence the structure, stability and function of molecules and materials. Despite the ubiquitous nature of vdW interactions, a simplified electrostatic model has been popularly adopted to explain common intermolecular interactions, especially those existing in π-involved systems. However, this classical model has come under fire in revealing specific issues such as substituent effects, due to its roughness; and it has been followed in past decades by sundry explanations which sometimes bring in nebulous descriptions. In this account, we try to summarise and present a unified model for describing and analysing the binding mechanism of such systems from the viewpoint of energy decomposition. We also emphasise a commonly ignored factor - orbital interaction, pointing out that the noncovalent intermolecular orbital interactions actually exhibit similar bonding and antibonding phenomena as those in covalent bonds.

Perturbation analyses of intermolecular interactions

NASA Astrophysics Data System (ADS)

Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Perturbation analyses of intermolecular interactions.

PubMed

Koyama, Yohei M; Kobayashi, Tetsuya J; Ueda, Hiroki R

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Regioselectivity of intermolecular Pauson-Khand reaction of aliphatic alkynes: experimental and theoretical study of the effect of alkyne polarization.

PubMed

Fager-Jokela, Erika; Muuronen, Mikko; Khaizourane, Héléa; Vázquez-Romero, Ana; Verdaguer, Xavier; Riera, Antoni; Helaja, Juho

2014-11-21

Generally judged poor electronic regioselectivity of alkyne insertion in intermolecular Pauson-Khand reaction (PKR) has severely restricted its synthetic applications. In our previous rational study concerning diarylalkynes (Fager-Jokela, E.; Muuronen, M.; Patzschke, M.; Helaja, J. J. Org. Chem. 2012, 77, 9134-9147), both experimental and theoretical results indicated that purely electronic factors, i.e., alkyne polarization via resonance effect, induced the observed modest regioselectivity. In the present work, we substantiate that the alkyne polarization via inductive effect can result notable, synthetically valuable regioselectivity. Computational study at DFT level was performed to disclose the electronic origin of the selectivity. Overall, the NBO charges of alkynes correlated qualitatively with regioisomer outcome. In a detailed computational PKR case study, the obtained Boltzmann distributions of the transition state (TS) populations correlate closely with experimental regioselectivity. Analysis of the TS-structures revealed that weak interactions, e.g., hydrogen bonding and steric repulsion, affect the regioselectivity and can easily override the electronic guidance.

Reliable prediction of three-body intermolecular interactions using dispersion-corrected second-order Møller-Plesset perturbation theory

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

Huang, Yuanhang; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu

2015-07-28

Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simplemore » model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O(N{sup 6}) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N{sup 5}) computational cost.« less

A Proposed Model for Protein Crystal Nucleation and Growth

NASA Technical Reports Server (NTRS)

Pusey, Marc; Curreri, Peter A. (Technical Monitor)

2002-01-01

How does one take a molecule, strongly asymmetric in both shape and charge distribution, and assemble it into a crystal? We propose a model for the nucleation and crystal growth process for tetragonal lysozyme, based upon fluorescence, light, neutron, and X-ray scattering data, size exclusion chromatography experiments, dialysis kinetics, AFM, and modeling of growth rate data, from this and other laboratories. The first species formed is postulated to be a 'head to side' dimer. Through repeating associations involving the same intermolecular interactions this grows to a 4(sub 3) helix structure, that in turn serves as the basic unit for nucleation and subsequent crystal growth. High salt attenuates surface charges while promoting hydrophobic interactions. Symmetry facilitates subsequent helix-helix self-association. Assembly stability is enhanced when a four helix structure is obtained, with each bound to two neighbors. Only two unique interactions are required. The first are those for helix formation, where the dominant interaction is the intermolecular bridging anion. The second is the anti-parallel side-by-side helix-helix interaction, guided by alternating pairs of symmetry related salt bridges along each side. At this stage all eight unique positions of the P4(sub3)2(sub 1),2(sub 1) unit cell are filled. The process is one of a) attenuating the most strongly interacting groups, such that b) the molecules begin to self-associate in defined patterns, so that c) symmetry is obtained, which d) propagates as a growing crystal. Simple and conceptually obvious in hindsight, this tells much about what we are empirically doing when we crystallize macromolecules. By adjusting the growth parameters we are empirically balancing the intermolecular interactions, preferentially attenuating the dominant strong (for lysozyme the charged groups) while strengthening the lesser strong (hydrophobic) interactions. In the general case for proteins the lack of a singularly defined association pathway may lead to formation of multiple species, i.e., amorphous precipitation. Weak interactions, such as hydrogen bonds, are promiscuous, serving to strengthen rather than define specific interactions. Participation in an interaction sequesters that surface from subsequent interactions, and we expect the strongest bonds to form first. This model, its basis, how it fits into the currently understood osmotic second virial coefficient approach to crystallization, and what it suggests will be discussed.

Crystal structure of (2E)-3-[4-(di-methyl-amino)-phen-yl]-1-(thio-phen-2-yl)prop-2-en-1-one.

PubMed

de Oliveira, Gabriela Porto; Bresolin, Leandro; Flores, Darlene Correia; de Farias, Renan Lira; de Oliveira, Adriano Bof

2017-04-01

The equimolar reaction between 4-(di-methyl-amino)-benzaldehyde and 2-acetyl-thio-phene in basic ethano-lic solution yields the title compound, C 15 H 15 NOS, whose mol-ecular structure matches the asymmetric unit. The mol-ecule is not planar, the dihedral angle between the aromatic and the thio-phene rings being 11.4 (2)°. In the crystal, mol-ecules are linked by C-H⋯O and weak C-H⋯S inter-actions along [100], forming R 2 2 (8) rings, and by weak C-H⋯O inter-actions along [010], forming chains with a C (6) graph-set motif. In addition, mol-ecules are connected into centrosymmetric dimers by weak C-H⋯π inter-actions, as indicated by the Hirshfeld surface analysis. The most important contributions for the crystal structure are the H⋯H (46.50%) and H⋯C (23.40%) inter-actions. The crystal packing resembles a herringbone arrangement when viewed along [100]. A mol-ecular docking calculation of the title compound with the neuraminidase enzyme was carried out. The enzyme shows ( ASN263 )N-H⋯O, ( PRO245 )C-H⋯ Cg (thio-phene ring) and ( AGR287 )C-H⋯N inter-molecular inter-actions with the title compound. The crystal structure was refined as a two-component twin with a fractional contribution to the minor domain of 0.0181 (8).

Vibrational coherence in polar solutions of Zn(II) tetrakis(N-methylpyridyl)porphyrin with Soret-band excitation: rapidly damped intermolecular modes with clustered solvent molecules and slowly damped intramolecular modes from the porphyrin macrocycle.

PubMed

Dillman, Kevin L; Shelly, Katherine R; Beck, Warren F

2009-04-30

Ground-state coherent wavepacket motions arising from intermolecular modes with clustered, first-shell solvent molecules were observed using the femtosecond dynamic absorption technique in polar solutions of Zn(II) meso-tetrakis(N-methylpyridyl)porphyrin (ZnTMPyP) with excitation in the Soret absorption band. As was observed previously in bacteriochlorophyll a solution, the pump-probe transients in ZnTMPyP solutions are weakly modulated by slowly damped (effective damping time gamma > 1 ps) features that are assigned to intramolecular modes, the skeletal normal modes of vibration of the porphyrin. The 40 cm(-1) and 215 cm(-1) modes from the metal-doming and metal-solvent-ligand modes, respectively, are members of this set of modulation components. A slowly damped 2-4 cm(-1) component is assigned to the internal rotation of the N-methylpyridyl rings with respect to the porphyrin macrocycle; this mode obtains strong resonance Raman intensity enhancement from an extensive delocalization of pi-electron density from the porphyrin in the ground state onto the rings in the pi* excited states. The dominant features observed in the pump-probe transients are a pair of rapidly damped (gamma < 250 fs) modulation components arising from intermolecular modes with solvent molecules. This structural assignment is supported by an isotope-dependent shift of the average mode frequencies in methanol and perdeuterated methanol. The solvent dependence of the mean intermolecular mode frequency is consistent with a van der Waals intermolecular potential that has significant contributions only from the London dispersion and induction interactions; ion-dipole or ion-induced-dipole terms do not make large contributions because the pi-electron density is not extensively delocalized onto the N-methylpyridyl rings. The modulation depth associated with the intermolecular modes exhibits a marked dependence on the electronic structure of the solvent that is probably related to the degree of covalency; the strongest modulations are observed in acetonitrile and dimethylsulfoxide. The results strongly support a structural assignment of the low-frequency modes that are coupled to the primary and secondary electron-transfer reactions in photosynthetic reaction centers to intermolecular modes between the redox-active chromophores and first-solvation shell groups from the surrounding protein, and an important additional function of the intermolecular modes in the stabilization of charged intermediates is suggested.

Point charge representation of multicenter multipole moments in calculation of electrostatic properties

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

1993-01-01

Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.

The Nature of the Dielectric Response of Methanol Revealed by the Terahertz Kerr Effect.

PubMed

Kampfrath, Tobias; Campen, R Kramer; Wolf, Martin; Sajadi, Mohsen

2018-03-15

The dielectric response of liquids in the terahertz (THz) and sub-THz frequency range arises from low-energy collective molecular motions, which are often strongly influenced by intermolecular interactions. To shed light on the microscopic origin of the THz dielectric response of the simplest alcohol, methanol, we resonantly excite this liquid with an intense THz electric-field pulse and monitor the relaxation of the induced optical birefringence. We find a unipolar THz-Kerr-effect signal which, in contrast to aprotic polar liquids, shows a weak coupling between the THz electric field and the permanent molecular dipole moment of the liquid. We assign this weak coupling to the restricted translational rather than rotational nature of the excited mode. Our approach opens a new avenue to the assignment of the dielectric spectrum of liquids to a microscopic origin.

Ultrasonic studies of intermolecular interactions in binary mixtures of 4-methoxy benzoin with various solvents: Excess molar functions of ultrasonic parameters at different concentrations and in different solvents.

PubMed

Thanuja, B; Nithya, G; Kanagam, Charles C

2012-11-01

Density (ρ), ultrasonic velocity (U), for the binary mixtures of 4-methoxy benzoin (4MB) with ethanol, chloroform, acetonitrile, benzene, and di-oxane were measured at 298K. The solute-solvent interactions and the effect of the polarity of the solvent on the type of intermolecular interactions are discussed here. From the above data, adiabatic compressibility (β), intermolecular free length (L(f)), acoustic impedance (Z), apparent molar volume (Ø), relative association (RA) have been calculated. Other useful parameters such as excess density, excess velocity and excess adiabatic compressibility have also been calculated. These parameters were used to study the nature and extent of intermolecular interactions between component molecules in the binary mixtures. Copyright © 2012 Elsevier B.V. All rights reserved.

What is measured by hyper-Rayleigh scattering from a liquid?

NASA Astrophysics Data System (ADS)

Rodriquez, Micheal B.; Shelton, David P.

2018-04-01

Polarization and angle dependence of hyper-Rayleigh scattering (HRS) measured for liquid acetonitrile and dimethyl sulfoxide (DMSO) is analyzed in terms of contributions from randomly oriented molecules and additional contributions produced during intermolecular collisions and induced by the electric field of dissolved ions. All three contributions show the effect of long-range correlation, and the correlation functions are determined using the HRS observations combined with the results of molecular dynamics simulations. HRS from acetonitrile is polarized transverse to the scattering vector. This is due to long-range molecular orientation correlation produced by the dipole-dipole interaction, and correlation at distances r > 100 nm must be included to account for the HRS observations. Analysis of the HRS measurements for acetonitrile determines the length scale a = 0.185 nm for the long-range longitudinal and transverse orientation correlation functions BL=-2 BT=a3/r3. Transverse polarized collision-induced HRS is also observed for acetonitrile, indicating long-range correlation of intermolecular modes. Strong longitudinal HRS is induced by the radial electric field of dissolved ions in acetonitrile. For DMSO, the angle between the molecular dipole and the vector part of the first hyperpolarizability tensor is about 100°. As a result, HRS from the randomly oriented molecules in DMSO is nearly unaffected by dipole correlation, and ion-induced HRS is weak. The strong longitudinal polarized HRS observed for DMSO is due to the collision-induced contribution, indicating long-range correlation of intermolecular modes. The HRS observations require correlation that has r-3 long-range asymptotic form, for molecular orientation and for intermolecular vibration and libration, for both acetonitrile and DMSO.

Learning about Intermolecular Interactions from the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.

2012-01-01

A clear understanding and appreciation of noncovalent interactions, especially hydrogen bonding, are vitally important to students of chemistry and the life sciences, including biochemistry, molecular biology, pharmacology, and medicine. The opportunities afforded by the IsoStar knowledge base of intermolecular interactions to enhance the…

Decomposition of Intermolecular Interactions in the Crystal Structure of Some Diacetyl Platinum(II) Complexes: Combined Hirshfeld, AIM, and NBO Analyses.

PubMed

Soliman, Saied M; Barakat, Assem

2016-12-06

Intermolecular interactions play a vital role in crystal structures. Therefore, we conducted a topological study, using Hirshfeld surfaces and atom in molecules (AIM) analysis, to decompose and analyze, respectively, the different intermolecular interactions in six hydrazone-diacetyl platinum(II) complexes. Using AIM and natural bond orbital (NBO) analyses, we determined the type, nature, and strength of the interactions. All the studied complexes contain C-H⋯O interactions, and the presence of bond critical points along the intermolecular paths underlines their significance. The electron densities (ρ(r)) at the bond critical points (0.0031-0.0156 e/a₀³) fall within the typical range for H-bonding interactions. Also, the positive values of the Laplacian of the electron density (∇²ρ(r)) revealed the depletion of electronic charge on the interatomic path, another characteristic feature of closed-shell interactions. The ratios of the absolute potential energy density to the kinetic energy density (| V (r)|/ G (r)) and ρ(r) are highest for the O2⋯H15-N3 interaction in [Pt(COMe)₂(2-pyCMe=NNH₂)] (1); hence, this interaction has the highest covalent character of all the O⋯H intermolecular interactions. Interestingly, in [Pt(COMe)₂(H₂NN=CMe-CMe=NNH₂)] (3), there are significant N-H⋯Pt interactions. Using the NBO method, the second-order interaction energies, E (2) , of these interactions range from 3.894 to 4.061 kJ/mol. Furthermore, the hybrid Pt orbitals involved in these interactions are comprised of d xy , d xz , and s atomic orbitals.

Intramolecular symmetry-adapted perturbation theory with a single-determinant wavefunction

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

Pastorczak, Ewa; Prlj, Antonio; Corminboeuf, Clémence, E-mail: clemence.corminboeuf@epfl.ch

2015-12-14

We introduce an intramolecular energy decomposition scheme for analyzing non-covalent interactions within molecules in the spirit of symmetry-adapted perturbation theory (SAPT). The proposed intra-SAPT approach is based upon the Chemical Hamiltonian of Mayer [Int. J. Quantum Chem. 23(2), 341–363 (1983)] and the recently introduced zeroth-order wavefunction [J. F. Gonthier and C. Corminboeuf, J. Chem. Phys. 140(15), 154107 (2014)]. The scheme decomposes the interaction energy between weakly bound fragments located within the same molecule into physically meaningful components, i.e., electrostatic-exchange, induction, and dispersion. Here, we discuss the key steps of the approach and demonstrate that a single-determinant wavefunction can already delivermore » a detailed and insightful description of a wide range of intramolecular non-covalent phenomena such as hydrogen bonds, dihydrogen contacts, and π − π stacking interactions. Intra-SAPT is also used to shed the light on competing intra- and intermolecular interactions.« less

Cell death versus cell survival instructed by supramolecular cohesion of nanostructures

NASA Astrophysics Data System (ADS)

Newcomb, Christina J.; Sur, Shantanu; Ortony, Julia H.; Lee, One-Sun; Matson, John B.; Boekhoven, Job; Yu, Jeong Min; Schatz, George C.; Stupp, Samuel I.

2014-02-01

Many naturally occurring peptides containing cationic and hydrophobic domains have evolved to interact with mammalian cell membranes and have been incorporated into materials for non-viral gene delivery, cancer therapy or treatment of microbial infections. Their electrostatic attraction to the negatively charged cell surface and hydrophobic interactions with the membrane lipids enable intracellular delivery or cell lysis. Although the effects of hydrophobicity and cationic charge of soluble molecules on the cell membrane are well known, the interactions between materials with these molecular features and cells remain poorly understood. Here we report that varying the cohesive forces within nanofibres of supramolecular materials with nearly identical cationic and hydrophobic structure instruct cell death or cell survival. Weak intermolecular bonds promote cell death through disruption of lipid membranes, while materials reinforced by hydrogen bonds support cell viability. These findings provide new strategies to design biomaterials that interact with the cell membrane.

Effects of sodium salt types on the intermolecular interaction of sodium alginate/antarctic krill protein composite fibers.

PubMed

Zhang, Rui; Guo, Jing; Liu, Yuanfa; Chen, Shuang; Zhang, Sen; Yu, Yue

2018-06-01

Sodium alginate (SA) and antarctic krill protein (AKP) were blended to fabricate the SA/AKP composite fibers by the conventional wet spinning method using 5% CaCl 2 as coagulation solution. The sodium salt was added to the SA/AKP solution to adjust the ionization degree and intermolecular interaction of composite system. The main purpose of this study is to investigate the influences of sodium salt types (NaCl, CH 3 COONa, Na 2 SO 4 ) on the intermolecular interaction of SA/AKP composite fibers. The intermolecular interaction, morphology, crystallinity, thermal stability and mechanical properties of SA/AKP composite fibers were analyzed by fourier transform infrared spectroscopy (FT-IR), scanning electron microscope (SEM), x-ray diffraction (XRD), thermogravimetric analysis (TGA). The results show that the types of sodium salt have obvious influences on the content of both β-sheet, intermolecular hydrogen bond, breaking strength and surface morphology in SA/AKP composite fibers, but have a negligible effect on the crystallinity and thermal stability. Copyright © 2018 Elsevier Ltd. All rights reserved.

π-stacking and C-X...D (X = H, NO2; D = O, π) interactions in the crystal network of both C-H...N and π-stacked dimers of 1,2-bis(4-bromophenyl)-1H-benzimidazole and 2-(4-bromophenyl)-1-(4-nitrophenyl)-1H-benzimidazole.

PubMed

González-Padilla, Jazmin E; Rosales-Hernández, Martha C; Padilla-Martínez, Itzia I; García-Báez, Efren V; Rojas-Lima, Susana; Salazar-Pereda, Veronica

2014-01-01

Molecules of 1,2-bis(4-bromophenyl)-1H-benzimidazole, C19H12Br2N2, (I), and 2-(4-bromophenyl)-1-(4-nitrophenyl)-1H-benzimidazole, C19H12BrN3O2, (II), are arranged in dimeric units through C-H...N and parallel-displaced π-stacking interactions favoured by the appropriate disposition of N- and C-bonded phenyl rings with respect to the mean benzimidazole plane. The molecular packing of the dimers of (I) and (II) arises by the concurrence of a diverse set of weak intermolecular C-X...D (X = H, NO2; D = O, π) interactions.

Diffusion within the cytoplasm: a mesoscale model of interacting macromolecules.

PubMed

Trovato, Fabio; Tozzini, Valentina

2014-12-02

Recent experiments carried out in the dense cytoplasm of living cells have highlighted the importance of proteome composition and nonspecific intermolecular interactions in regulating macromolecule diffusion and organization. Despite this, the dependence of diffusion-interaction on physicochemical properties such as the degree of poly-dispersity and the balance between steric repulsion and nonspecific attraction among macromolecules was not systematically addressed. In this work, we study the problem of diffusion-interaction in the bacterial cytoplasm, combining theory and experimental data to build a minimal coarse-grained representation of the cytoplasm, which also includes, for the first time to our knowledge, the nucleoid. With stochastic molecular-dynamics simulations of a virtual cytoplasm we are able to track the single biomolecule motion, sizing from 3 to 80 nm, on submillisecond-long trajectories. We demonstrate that the size dependence of diffusion coefficients, anomalous exponents, and the effective viscosity experienced by biomolecules in the cytoplasm is fine-tuned by the intermolecular interactions. Accounting only for excluded volume in these potentials gives a weaker size-dependence than that expected from experimental data. On the contrary, adding nonspecific attraction in the range of 1-10 thermal energy units produces a stronger variation of the transport properties at growing biopolymer sizes. Normal and anomalous diffusive regimes emerge straightforwardly from the combination of high macromolecular concentration, poly-dispersity, stochasticity, and weak nonspecific interactions. As a result, small biopolymers experience a viscous cytoplasm, while the motion of big ones is jammed because the entanglements produced by the network of interactions and the entropic effects caused by poly-dispersity are stronger. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

On the roles of close shell interactions in the structure of acyl-substituted hydrazones: An experimental and theoretical approach

NASA Astrophysics Data System (ADS)

Saeed, Aamer; Ifzan Arshad, M.; Bolte, Michael; Fantoni, Adolfo C.; Delgado Espinoza, Zuly Y.; Erben, Mauricio F.

2016-03-01

The 2-(phenyl-hydrazono)-succinic acid dimethyl ester compound was synthesized by reacting phenylhydrazine with dimethylacetylene dicarboxylate at room temperature and characterized by elemental analysis, infrared, Raman, 1H and 13C NMR spectroscopies and mass spectrometry. Its solid state structure was determined by X-ray diffraction methods. The X-ray structure determination corroborates that the molecule is present in the crystal as the hydrazone tautomer, probably favored by a strong intramolecular N-H···Odbnd C hydrogen bond occurring between the carbonyl (-Cdbnd O) and the hydrazone -Cdbnd N-NH- groups. A substantial fragment of the molecular skeleton is planar due to an extended π-bonding delocalization. The topological analysis of the electron densities (Atom in Molecule, AIM) allows characterization of intramolecular N-H···O interaction, that can be classified as a resonant assisted hydrogen bond (RAHB). Moreover, the Natural Bond Orbital population analysis confirms that a strong hyperconjugative lpO1 → σ*(N2-H) remote interaction between the C2dbnd O1 and N2-H groups takes place. Periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Weak intermolecular interactions determine the crystal packing, and the prevalence of non-directional dispersive contributions are inferred on topological grounds. The IR spectrum of the crystalline compound was investigated by means of density functional theory calculations carried out with periodic boundary conditions on the crystal, showing excellent agreement between theory and the experiments. The vibrational assignment is complemented with the analysis of the Raman spectrum.

Synthesis of Polyvinylpyrrolidone (PVP)-Green Tea Extract Composite Nanostructures using Electrohydrodynamic Spraying Technique

NASA Astrophysics Data System (ADS)

Kamaruddin; Edikresnha, D.; Sriyanti, I.; Munir, M. M.; Khairurrijal

2017-05-01

Green Tea Extract (GTE) as an active substance has successfully loaded to PVP nanostructures using electrohydrodynamic spraying technique. The precursor solution was the mixture of ethanolic polyvinylpyrrolidone (PVP) with a molecular weight of 1,300 kg/mol and ethanolic GTE solutions at a weight concentration of 4 wt.% and 2 wt.%, respectively, and it was estimated that the entanglement number was 2. The electrospraying was conducted at the voltage of 15 kV, the flow rate of 10 µL/min., and the distance between the collector and the tip of the nozzle of 10 cm. The SEM images showed that the PVP/GTE nanostructures had a combination of agglomerated beads (less spherical particles) and nanofibers. This occurred because if the PVP concentration is low, the PVP/GTE composite has weak core structures that cause the shell to be easily agglomerated each other. The intermolecular interaction between PVP and GTE in the PVP/GTE nanostructures occurred as confirmed by the peak at 3396 cm-1, which is the carboxyl group, proving that the PVP/GTE nanostructures contained water, alcohols, and phenols. The peak at 1040 cm-1, which is the stretching of C-O group in amino acid, gave another proof to the intermolecular interaction.

Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips

NASA Astrophysics Data System (ADS)

Mönig, Harry; Amirjalayer, Saeed; Timmer, Alexander; Hu, Zhixin; Liu, Lacheng; Díaz Arado, Oscar; Cnudde, Marvin; Strassert, Cristian Alejandro; Ji, Wei; Rohlfing, Michael; Fuchs, Harald

2018-05-01

Atomic force microscopy is an impressive tool with which to directly resolve the bonding structure of organic compounds1-5. The methodology usually involves chemical passivation of the probe-tip termination by attaching single molecules or atoms such as CO or Xe (refs 1,6-9). However, these probe particles are only weakly connected to the metallic apex, which results in considerable dynamic deflection. This probe particle deflection leads to pronounced image distortions, systematic overestimation of bond lengths, and in some cases even spurious bond-like contrast features, thus inhibiting reliable data interpretation8-12. Recently, an alternative approach to tip passivation has been used in which slightly indenting a tip into oxidized copper substrates and subsequent contrast analysis allows for the verification of an oxygen-terminated Cu tip13-15. Here we show that, due to the covalently bound configuration of the terminal oxygen atom, this copper oxide tip (CuOx tip) has a high structural stability, allowing not only a quantitative determination of individual bond lengths and access to bond order effects, but also reliable intermolecular bond characterization. In particular, by removing the previous limitations of flexible probe particles, we are able to provide conclusive experimental evidence for an unusual intermolecular N-Au-N three-centre bond. Furthermore, we demonstrate that CuOx tips allow the characterization of the strength and configuration of individual hydrogen bonds within a molecular assembly.

Millimeter Wave Spectrum of the Weakly Bound Complex CH2═CHCN·H2O: Structure, Dynamics, and Implications for Astronomical Search.

PubMed

Calabrese, Camilla; Vigorito, Annalisa; Maris, Assimo; Mariotti, Sergio; Fathi, Pantea; Geppert, Wolf D; Melandri, Sonia

2015-12-03

The weakly bound 1:1 complex between acrylonitrile (CH2═CHCN) and water has been characterized spectroscopically in the millimeter wave range (59.6-74.4 GHz) using a Free Jet Absorption Millimeter Wave spectrometer. Precise values of the rotational and quartic centrifugal distortion constants have been obtained from the measured frequencies of the normal and isotopically substituted water moiety (DOH, DOD, H(18)OH). Structural parameters have been estimated from the rotational constants and their differences among isotopologues: the complex has a planar structure with the two subunits held together by a O-H···N (2.331(3) Å) and a C-H···O (2.508(4) Å) interaction. The ab initio intermolecular binding energy, obtained at the counterpoise corrected MP2/aug-cc-pVTZ level of calculation, is De = 24.4 kJ mol(-1).

High pressure structural, elastic and vibrational properties of green energetic oxidizer ammonium dinitramide

NASA Astrophysics Data System (ADS)

Yedukondalu, N.; Ghule, Vikas D.; Vaitheeswaran, G.

2016-08-01

Ammonium DiNitramide (ADN) is one of the most promising green energetic oxidizers for future rocket propellant formulations. In the present work, we report a detailed theoretical study on structural, elastic, and vibrational properties of the emerging oxidizer under hydrostatic compression using various dispersion correction methods to capture weak intermolecular (van der Waals and hydrogen bonding) interactions. The calculated ground state lattice parameters, axial compressibilities, and equation of state are in good accord with the available experimental results. Strength of intermolecular interactions has been correlated using the calculated compressibility curves and elastic moduli. Apart from this, we also observe discontinuities in the structural parameters and elastic constants as a function of pressure. Pictorial representation and quantification of intermolecular interactions are described by the 3D Hirshfeld surfaces and 2D finger print maps. In addition, the computed infra-red (IR) spectra at ambient pressure reveal that ADN is found to have more hygroscopic nature over Ammonium Perchlorate (AP) due to the presence of strong hydrogen bonding. Pressure dependent IR spectra show blue- and red-shift of bending and stretching frequencies which leads to weakening and strengthening of the hydrogen bonding below and above 5 GPa, respectively. The abrupt changes in the calculated structural, mechanical, and IR spectra suggest that ADN might undergo a first order structural transformation to a high pressure phase around 5-6 GPa. From the predicted detonation properties, ADN is found to have high and low performance characteristics (DCJ = 8.09 km/s and PCJ = 25.54 GPa) when compared with ammonium based energetic oxidizers (DCJ = 6.50 km/s and PCJ = 17.64 GPa for AP, DCJ = 7.28 km/s and PCJ = 18.71 GPa for ammonium nitrate) and well-known secondary explosives for which DCJ = ˜8-10 km/s and PCJ = ˜30-50 GPa, respectively.

Identification and measurement of intermolecular interaction in polyester/polystyrene blends by FTIR-photoacoustic spectrometry

USDA-ARS?s Scientific Manuscript database

Fourier transform infrared photoacoustic spectrometry was used to reveal and identify n-p type intermolecular interaction formed in plastic comprising binary blends of polystyrene and a biodegradable polymer, either polylactic acid, polycaprolactone or poly(tetramethyleneadipate-co-terephthalate)....

Molecular electrostatics for probing lone pair-π interactions.

PubMed

Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

2013-11-14

An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

Molecular recognition of organic ammonium ions in solution using synthetic receptors

PubMed Central

Späth, Andreas

2010-01-01

Summary Ammonium ions are ubiquitous in chemistry and molecular biology. Considerable efforts have been undertaken to develop synthetic receptors for their selective molecular recognition. The type of host compounds for organic ammonium ion binding span a wide range from crown ethers to calixarenes to metal complexes. Typical intermolecular interactions are hydrogen bonds, electrostatic and cation–π interactions, hydrophobic interactions or reversible covalent bond formation. In this review we discuss the different classes of synthetic receptors for organic ammonium ion recognition and illustrate the scope and limitations of each class with selected examples from the recent literature. The molecular recognition of ammonium ions in amino acids is included and the enantioselective binding of chiral ammonium ions by synthetic receptors is also covered. In our conclusion we compare the strengths and weaknesses of the different types of ammonium ion receptors which may help to select the best approach for specific applications. PMID:20502608

X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data

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

Mou, Q.; Benmore, C. J.; Yarger, J. L.

2015-06-01

XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained. XISF has been optimized for performance and can separate intermolecular structure factors of complex molecules.

X-ray Intermolecular Structure Factor ( XISF ): separation of intra- and intermolecular interactions from total X-ray scattering data

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

Mou, Q.; Benmore, C. J.; Yarger, J. L.

2015-05-09

XISFis a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained.XISFhas been optimized for performance and can separate intermolecular structure factors of complex molecules.

Thioarsenides: A case for long-range Lewis acid-base-directed van der Waals interactions

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

Gibbs, Gerald V.; Wallace, Adam F.; Downs, R. T.

2011-04-01

Electron density distributions, bond paths, Laplacian and local energy density properties have been calculated for a number of As4Sn (n = 3,4,5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis base regions) with aligned regions of locally depleted electron density (Lewis acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for severalmore » other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long range Lewis acid-base directed van der Waals interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and β-AsS and the distorted hexagonal close-packed arrays adopted by α- and β-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.« less

Investigation of intermolecular interaction of binary mixture of acrylonitrile with bromobenzene

NASA Astrophysics Data System (ADS)

Deshmukh, S. D.; Pattebahadur, K. L.; Mohod, A. G.; Patil, S. S.; Khirade, P. W.

2018-04-01

In this paper, study of binary mixture of Acrylonitrile (ACN)with Bromobenzene(BB) has been carried out at eleven concentrations at room temperature. The determined density(ρ) and refractive index (nD) values of binary mixture are used to calculate the excess properties of mixture over the entire composition range. The aforesaid parameters are used to calculate excess parameters and fitted to the Redlich-Kister equation to determine the bj coefficients. From the above parameters, intermolecular interaction and dynamics of molecules of binary mixture at molecular level are discussed. The Conformational analysis of the intermolecular interaction between Acrylonitrile and Bromobenzene is supported by the FTIR spectra.

Acid-Base Interactions of Polystyrene Sulfonic Acid in Amorphous Solid Dispersions Using a Combined UV/FTIR/XPS/ssNMR Study.

PubMed

Song, Yang; Zemlyanov, Dmitry; Chen, Xin; Nie, Haichen; Su, Ziyang; Fang, Ke; Yang, Xinghao; Smith, Daniel; Byrn, Stephen; Lubach, Joseph W

2016-02-01

This study investigates the potential drug-excipient interactions of polystyrene sulfonic acid (PSSA) and two weakly basic anticancer drugs, lapatinib (LB) and gefitinib (GB), in amorphous solid dispersions. Based on the strong acidity of the sulfonic acid functional group, PSSA was hypothesized to exhibit specific intermolecular acid-base interactions with both model basic drugs. Ultraviolet (UV) spectroscopy identified red shifts, which correlated well with the color change observed in lapatinib-PSSA solutions. Fourier transform infrared (FTIR) spectra suggest the protonation of the quinazoline nitrogen atom in both model compounds, which agrees well with data from the crystalline ditosylate salt of lapatinib. X-ray photoelectron spectroscopy (XPS) detected increases in binding energy of the basic nitrogen atoms in both lapatinib and gefitinib, strongly indicating protonation of these nitrogen atoms. (15)N solid-state NMR spectroscopy provided direct spectroscopic evidence for protonation of the quinazoline nitrogen atoms in both LB and GB, as well as the secondary amine nitrogen atom in LB and the tertiary amine nitrogen atom in GB. The observed chemical shifts in the LB-PSSA (15)N spectrum also agree very well with the lapatinib ditosylate salt where proton transfer is known. Additionally, the dissolution and physical stability behaviors of both amorphous solid dispersions were examined. PSSA was found to significantly improve the dissolution of LB and GB and effectively inhibit the crystallization of LB and GB under accelerated storage conditions due to the beneficial strong intermolecular acid-base interaction between the sulfonic acid groups and basic nitrogen centers.

Study of intermolecular interactions in binary mixtures of 2'-chloro-4-methoxy-3-nitro benzil in various solvents and at different concentrations by the measurement of acoustic properties.

PubMed

Nithya, G; Thanuja, B; Kanagam, Charles C

2013-01-01

Density (ρ), ultrasonic velocity (u), adiabatic compressibility (β), apparent molar volume (Ø), acoustic impedance (Z), intermolecular free length (L(f)), relative association (RA) of binary mixtures of 2'-chloro-4-methoxy-3-nitro benzil (abbreviated as 2CBe) in ethanol, acetonitrile, chloroform, dioxane and benzene were measured at different concentrations at 298 K. Several useful parameters such as excess density, excess ultrasonic velocity, excess adiabatic compressibility, excess apparent molar volume, excess acoustic impedance and excess intermolecular free length have been calculated. These parameters are used to explain the nature of intermolecular interactions taking place in the binary mixture. The above study is useful in understanding the solute--solvent interactions occurring in different concentrations at room temperature. Copyright © 2012 Elsevier B.V. All rights reserved.

Rationalizing Tight Ligand Binding through Cooperative Interaction Networks

PubMed Central

2011-01-01

Small modifications of the molecular structure of a ligand sometimes cause strong gains in binding affinity to a protein target, rendering a weakly active chemical series suddenly attractive for further optimization. Our goal in this study is to better rationalize and predict the occurrence of such interaction hot-spots in receptor binding sites. To this end, we introduce two new concepts into the computational description of molecular recognition. First, we take a broader view of noncovalent interactions and describe protein–ligand binding with a comprehensive set of favorable and unfavorable contact types, including for example halogen bonding and orthogonal multipolar interactions. Second, we go beyond the commonly used pairwise additive treatment of atomic interactions and use a small world network approach to describe how interactions are modulated by their environment. This approach allows us to capture local cooperativity effects and considerably improves the performance of a newly derived empirical scoring function, ScorpionScore. More importantly, however, we demonstrate how an intuitive visualization of key intermolecular interactions, interaction networks, and binding hot-spots supports the identification and rationalization of tight ligand binding. PMID:22087588

An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

PubMed Central

Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

2012-01-01

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

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.

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

PubMed

Mereghetti, Paolo; Wade, Rebecca C

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Supramolecular binding and separation of hydrocarbons within a functionalized porous metal–organic framework

DOE PAGES

Yang, Sihai; Ramirez-Cuesta, Anibal J.; Newby, Ruth; ...

2014-12-01

Supramolecular interactions are fundamental to host–guest binding in many chemical and biological processes. Direct visualization of such supramolecular interactions within host–guest systems is extremely challenging, but crucial to understanding their function. Within this paper, we report a comprehensive study that combines neutron scattering, synchrotron X-ray and neutron diffraction, and computational modelling to define the detailed binding at a molecular level of acetylene, ethylene and ethane within the porous host NOTT-300. This study reveals simultaneous and cooperative hydrogen-bonding, π···π stacking interactions and intermolecular dipole interactions in the binding of acetylene and ethylene to give up to 12 individual weak supramolecular interactionsmore » aligned within the host to form an optimal geometry for the selective binding of hydrocarbons. In addition, we also report the cooperative binding of a mixture of acetylene and ethylene within the porous host, together with the corresponding breakthrough experiments and analysis of adsorption isotherms of gas mixtures.« less

Study of Pair and many-body interactions in rare-gas halide atom clusters using negative ion zero electron kinetic energy (ZEKE) and threshold photodetachment spectroscopy

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

Yourshaw, Ivan

1998-07-09

The diatomic halogen atom-rare gas diatomic complexes KrBr -, XeBr -, and KrCl - are studied in this work by zero electron kinetic energy (ZEKE) spectroscopy in order to characterize the weak intermolecular diatomic potentials of these species. Also, the ZEKE and threshold photodetachment spectra of the polyatomic clusters Ar nBr - (n = 2-9) and Ar nI - (n = 2-19) are studied to obtain information about the non-additive effects on the interactions among the atoms. This work is part of an ongoing effort to characterize the pair and many-body potentials of the complete series of rare gas halidemore » clusters. In these studies we obtain information about both the anionic and neutral clusters.« less

Synthetic/Biosynthetic Phase Transfer Polymers for Pollution Minimization, Remediation, and Waste Management

DTIC Science & Technology

1994-01-01

in the viscosity profile is observed. DAMAB induces strong intermolecular associations via hydrophobic interactions . When copolymers of comparable...techniques such as viscosity studies. The AM/DAMAB copolymer series also interacts with surfactants in an interesting manner.’ The surface tension of...in polymer dimensions as hydrophobe is added. The shape of the viscosity curves does not suggest intermolecular interactions , as in typical

Study of intermolecular interactions in binary mixtures of ethanol in methanol

NASA Astrophysics Data System (ADS)

Maharolkar, Aruna P.; Khirade, P. W.; Murugkar, A. G.

2016-05-01

Present paper deals with study of physicochemical properties like viscosity, density and refractive index for the binary mixtures of ethanol and methanol over the entire concentration range were measured at 298.15 K. The experimental data further used to determine the excess properties viz. excess molar volume, excess viscosity, excess molar refraction. The values of excess properties further fitted with Redlich-Kister (R-K Fit) equation to calculate the binary coefficients and standard deviation. The resulting excess parameters are used to indicate the presence of intermolecular interactions and strength of intermolecular interactions between the molecules in the binary mixtures. Excess parameters indicate structure making factor in the mixture predominates in the system.

Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Study of molecular interactions in binary mixtures of 2-chloro-4'methoxy benzoin with various solvents through ultrasonic speed measurements

NASA Astrophysics Data System (ADS)

Thanuja, B.; Kanakam, C.; Nithya, G.

2013-12-01

Density ( ρ) and ultrasonic velocity ( U), for binary mixtures of 2-chloro-4'-methoxy benzoin with ethanol, chloroform, acetonitrile, benzene and 1,4-dioxane of different compositions have been measured at 298 K and explanation of solute solvent interactions and effect of polarity of the solvent on type of interactions are presented in this paper. From the above data, adiabatic compressibility ( β), intermolecular free length ( L f ) and relative association ( R A ) have been calculated. Other useful parameters such as excess density, excess velocity, excess intermolecular freelength and excess adiabatic compressibility have also been calculated. These parameters have been used to study the nature and extent of intermolecular interactions between component molecules in present binary mixtures.

Ferrocenylaniline based amide analogs of methoxybenzoic acids: Synthesis, structural characterization and butyrylcholinesterase (BChE) inhibition studies

NASA Astrophysics Data System (ADS)

Altaf, Ataf Ali; Kausar, Samia; Hamayun, Muhammad; Lal, Bhajan; Tahir, Muhammad Nawaz; Badshah, Amin

2017-10-01

Three new ferrocene based amides were synthesized with slight structural difference. The general formula of the amides is C5H5FeC5H4C6H4NHCOC6H4(OCH3). The synthesized compounds were characterized by instrumental techniques like elemental analysis, FTIR and NMR spectroscopy. Structure of the two compounds was also studied by single crystal X-rays diffraction analysis. Structural studies provide the evidence that pMeO (one of the synthesized compounds) is an example of amides having no intermolecular hydrogen bonding in solid structure. In the BChE inhibition assay, compound (oMeO) having strong intermolecular force in the solid structure is less active than the compound (pMeO) with weak intermolecular forces in the solid structure. The docking studies proved that hydrogen bonding between inhibitor and BChE enzyme is of more importance for the activity, rather than intermolecular hydrogen bonding in the solid structure of inhibitor.

Connecting Protein Structure to Intermolecular Interactions: A Computer Modeling Laboratory

ERIC Educational Resources Information Center

Abualia, Mohammed; Schroeder, Lianne; Garcia, Megan; Daubenmire, Patrick L.; Wink, Donald J.; Clark, Ginevra A.

2016-01-01

An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several…

Fundamental relation between molecular geometry and real-space topology. Combined AIM, ELI-D, and ASF analysis of hapticities and intramolecular hydrogen-hydrogen bonds in zincocene-related compounds.

PubMed

Mebs, Stefan; Chilleck, Maren Annika; Meindl, Kathrin; Hübschle, Christian Bertram

2014-06-19

Despite numerous advanced and widely distributed bonding theories such as MO, VB, NBO, AIM, and ELF/ELI-D, complex modes of bonding such as M-Cp*((R)) interactions (hapticities) in asymmetrical metallocenes or weak intramolecular interactions (e.g., hydrogen-hydrogen (H···H) bonds) still remain a challenge for these theories in terms of defining whether or not an atom-atom interaction line (a "chemical bond") should be drawn. In this work the intramolecular Zn-C(Cp*(R)) (R = Me, -(CH2)2NMe2, and -(CH2)3NMe2) and H···H connectivity of a systematic set of 12 zincocene-related compounds is analyzed in terms of AIM and ELI-D topology combined with the recently introduced aspherical stockholder fragment (ASF) surfaces. This computational analysis unravels a distinct dependency of the AIM and ELI-D topology against the molecular geometry for both types of interactions, which confirms and extends earlier findings on smaller sets of compounds. According to these results the complete real-space topology including strong, medium, and weak interactions of very large compounds such as proteins may be reliably predicted by sole inspection of accurately determined molecular geometries, which would on the one hand afford new applications (e.g., accurate estimation of numbers, types, and strengths of intra- and intermolecular interactions) and on the other hand have deep implications on the significance of the method.

N-(2,3-Dimethyl-phen-yl)-4-hydr-oxy-2-methyl-2H-1,2-benzothia-zine-3-carboxamide 1,1-dioxide.

PubMed

Siddiqui, Waseeq Ahmad; Bukahari, Iftikhar Hussain; Zia-Ur-Rehman, Muhammad; Khan, Islam Ullah; Tizzard, Graham John

2009-02-28

In the crystal structure of the title compound, C(18)H(18)N(2)O(4)S, the thia-zine ring adopts a distorted half-chair conformation. 1,2-Benzothia-zines of this kind have a wide range of biological activities and are mainly used as medicines in the treatment of inflammation and rheumatoid arthritis. The enolic H atom is involved in an intra-molecular O-H⋯O hydrogen bond, forming a six-membered ring. The mol-ecules arrange themselves into centrosymmetric dimers by means of inter-molecular N-H⋯O hydrogen bonds. A weak inter-molcular C-H⋯O inter-action is also present.

N,N-Dimethyl-N-propyl-propan-1-aminium chloride monohydrate.

PubMed

Kärnä, Minna; Lahtinen, Manu; Valkonen, Jussi

2008-10-11

The title compound, C(8)H(20)N(+)·Cl(-)·H(2)O, has been prepared by a simple one-pot synthesis route followed by anion exchange using resin. In the crystal structure, the cations are packed in such a way that channels exist parallel to the b axis. These channels are filled by the anions and water mol-ecules, which inter-act via O-H⋯Cl hydrogen bonds [O⋯Cl = 3.285 (3) and 3.239 (3) Å] to form helical chains. The cations are involved in weak inter-molecular C-H⋯Cl and C-H⋯O hydrogen bonds. The title compound is not isomorphous with the bromo or iodo analogues.

A Scalable Implementation of Van der Waals Density Functionals

NASA Astrophysics Data System (ADS)

Wu, Jun; Gygi, Francois

2010-03-01

Recently developed Van der Waals density functionals[1] offer the promise to account for weak intermolecular interactions that are not described accurately by local exchange-correlation density functionals. In spite of recent progress [2], the computational cost of such calculations remains high. We present a scalable parallel implementation of the functional proposed by Dion et al.[1]. The method is implemented in the Qbox first-principles simulation code (http://eslab.ucdavis.edu/software/qbox). Application to large molecular systems will be presented. [4pt] [1] M. Dion et al. Phys. Rev. Lett. 92, 246401 (2004).[0pt] [2] G. Roman-Perez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009).

Elasticity and Strength of Biomacromolecular Crystals: Lysozyme

NASA Technical Reports Server (NTRS)

Holmes, A. M.; Witherow, W. K.; Chen, L. Q.; Chernov, A. A.

2003-01-01

The static Young modulus, E = 0.1 to 0.5 GPa, the crystal critical strength (sigma(sub c)) and its ratio to E,sigma(sub c)/E is approximately 10(exp 3), were measured for the first time for non cross-linked lysozyme crystals in solution. By using a triple point bending apparatus, we also demonstrated that the crystals were purely elastic. Softness of protein crystals built of hard macromolecules (26 GPa for lysozyme) is explained by the large size of the macromolecules as compared to the range of intermolecular forces and by the weakness of intermolecular bonds as compared to the peptide bond strength. The relatively large reported dynamic elastic moduli (approximately 8 GPa) from resonance light scattering should come from averaging over the moduli of intracrystalline water and intra- and intermolecular bonding.

Communication: THz absorption spectrum of the CO2-H2O complex: observation and assignment of intermolecular van der Waals vibrations.

PubMed

Andersen, J; Heimdal, J; Mahler, D W; Nelander, B; Larsen, R Wugt

2014-03-07

Terahertz absorption spectra have been recorded for the weakly bound CO2-H2O complex embedded in cryogenic neon matrices at 2.8 K. The three high-frequency van der Waals vibrational transitions associated with out-of-plane wagging, in-plane rocking, and torsional motion of the isotopic H2O subunit have been assigned and provide crucial observables for benchmark theoretical descriptions of this systems' flat intermolecular potential energy surface. A (semi)-empirical value for the zero-point energy of 273 ± 15 cm(-1) from the class of intermolecular van der Waals vibrations is proposed and the combination with high-level quantum chemical calculations provides a value of 726 ± 15 cm(-1) for the dissociation energy D0.

Correlation of Intermolecular Acyl Transfer Reactivity with Noncovalent Lattice Interactions in Molecular Crystals: Toward Prediction of Reactivity of Organic Molecules in the Solid State.

PubMed

Krishnaswamy, Shobhana; Shashidhar, Mysore S

2018-04-06

Intermolecular acyl transfer reactivity in several molecular crystals was studied, and the outcome of the reactivity was analyzed in the light of structural information obtained from the crystals of the reactants. Minor changes in the molecular structure resulted in significant variations in the noncovalent interactions and packing of molecules in the crystal lattice, which drastically affected the facility of the intermolecular acyl transfer reactivity in these crystals. Analysis of the reactivity vs crystal structure data revealed dependence of the reactivity on electrophile···nucleophile interactions and C-H···π interactions between the reacting molecules. The presence of these noncovalent interactions augmented the acyl transfer reactivity, while their absence hindered the reactivity of the molecules in the crystal. The validity of these correlations allows the prediction of intermolecular acyl transfer reactivity in crystals and co-crystals of unknown reactivity. This crystal structure-reactivity correlation parallels the molecular structure-reactivity correlation in solution-state reactions, widely accepted as organic functional group transformations, and sets the stage for the development of a similar approach for reactions in the solid state.

Morphology and the Strength of Intermolecular Contact in Protein Crystals

NASA Technical Reports Server (NTRS)

Matsuura, Yoshiki; Chernov, Alexander A.

2002-01-01

The strengths of intermolecular contacts (macrobonds) in four lysozyme crystals were estimated based on the strengths of individual intermolecular interatomic interaction pairs. The periodic bond chain of these macrobonds accounts for the morphology of protein crystals as shown previously. Further in this paper, the surface area of contact, polar coordinate representation of contact site, Coulombic contribution on the macrobond strength, and the surface energy of the crystal have been evaluated. Comparing location of intermolecular contacts in different polymorphic crystal modifications, we show that these contacts can form a wide variety of patches on the molecular surface. The patches are located practically everywhere on this surface except for the concave active site. The contacts frequently include water molecules, with specific intermolecular hydrogen-bonds on the background of non-specific attractive interactions. The strengths of macrobonds are also compared to those of other protein complex systems. Making use of the contact strengths and taking into account bond hydration we also estimated crystal-water interfacial energies for different crystal faces.

Exploring contribution of intermolecular interactions in supramolecular layered assembly of naphthyridine co-crystals: Insights from Hirshfeld surface analysis of their crystalline states

NASA Astrophysics Data System (ADS)

Seth, Saikat Kumar; Das, Nirmal Kumar; Aich, Krishnendu; Sen, Debabrata; Fun, Hoong-Kun; Goswami, Shyamaprasad

2013-09-01

Co-crystals of 1a and 1b have been prepared by slow evaporation of the solutions of mixtures of 2,7-dimethyl-1,8-naphthyridine (1), urea (a) and thiourea (b). The structures of the complexes are determined by the single crystal X-ray diffraction and a detailed investigation of the crystal packing and classification of intermolecular interactions is presented by means of Hirshfeld surface analysis which is of considerable current interest in crystal engineering. The X-ray study reveals that the co-crystal formers are envisioned to produce N-H⋯N hydrogen bond as well as N-H⋯O/N-H⋯S pair-wise hydrogen bonds and also the weaker aromatic π⋯π interactions which cooperatively take part in the crystal packing. The recurring feature of the self-assembly in the compounds is the appearance of the molecular ribbon through multiple hydrogen bonding which are further stacked into molecular layers by π⋯π stacking interactions. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D Fingerprint plots have been used to examine molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

From intermolecular interactions to structures and properties of a novel cocrystal explosive: a first-principles study.

PubMed

Zhang, Lei; Wu, Ji-Zhou; Jiang, Sheng-Li; Yu, Yi; Chen, Jun

2016-09-29

By employing a first-principles method, we conducted a thorough study on a novel cocrystal explosive 1 : 1 NTO : TZTN and gained insight into the interaction-structure-property interrelationship. Mulliken bond orders, Hirshfeld surfaces, intermolecular binding energies, packing coefficients, and oxygen balance were calculated to analyze the intermolecular interactions and structures of the cocrystal explosive. The cocrystallization of NTO and TZTN molecules enhances the intermolecular binding force, which drives the synthesis of the cocrystal. However, the cocrystallization decreases the molecular packing density along the closest packed directions, which reduces the density by 10.5% and deteriorates the oxygen balance. All of these lead to a reduction in the detonation performance compared to NTO explosives. We have also proposed a new method to evaluate the impact sensitivity according to the lattice dynamics calculation. The cocrystal explosive has a lower impact sensitivity than TZTN but higher than NTO, which agrees well with experiments.

Vibration-rotation-tunneling spectroscopy of the van der Waals Bond: A new look at intermolecular forces

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

Cohen, R.C.; Saykally, R.J.

Measurements of the low-frequency van der Waals vibrations in weakly bound complexes by high-resolution laser spectroscopy provide a means to probe intermolecular forces at unprecedented levels of detail and precision. Several new methods are presently being used to record vibration/rotation-tunneling (VRT) transitions associated with the motions of the weak bonds in van der Waals clusters. The most direct measurements are those probing only the van der Waals modes themselves, which occur at far-infrared wavelengths. This article presents a review of the information on both intramolecular forces and intramolecular dynamics that has been obtained from far-infrared VRT spectra of 18 complexesmore » during the past several years. Some rotationally resolved measurements of van der Waals modes observed in combination with electronic or vibrational excitation are also discussed. 185 refs., 15 figs., 1 tab.« less

Communication: Density functional theory overcomes the failure of predicting intermolecular interaction energies

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

Podeszwa, Rafal; Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716; Szalewicz, Krzysztof

2012-04-28

Density-functional theory (DFT) revolutionized the ability of computational quantum mechanics to describe properties of matter and is by far the most often used method. However, all the standard variants of DFT fail to predict intermolecular interaction energies. In recent years, a number of ways to go around this problem has been proposed. We show that some of these approaches can reproduce interaction energies with median errors of only about 5% in the complete range of intermolecular configurations. Such errors are comparable to typical uncertainties of wave-function-based methods in practical applications. Thus, these DFT methods are expected to find broad applicationsmore » in modelling of condensed phases and of biomolecules.« less

The study of intermolecular interactions in NLO crystal melaminium chloride hemihydrate using DFT simulation and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Sangeetha, K.; Kumar, V. R. Suresh; Marchewka, M. K.; Binoy, J.

2018-05-01

Since, the intermolecular interactions play a crucial role in the formation of crystalline network, its analysis throws light on structure dependent crystalline properties. In the present study, DFT based vibrational spectral investigation has been performed in the stretching region (3500 cm-1 - 2800 cm-1) of IR and Raman spectra of melaminium chloride hemihydrates. The intermolecular interaction has been investigated by analyzing the half width of the OH and NH stretching profile of the deconvoluted spectra. Correlation of vibrational spectra with Hirshfeld surface analysis and finger print plot has been contemplated and molecular docking studies has been performed on melaminium chloride hemihydrate to assess its role in the drug transport mechanism and toxicity to human body.

Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide−noble-gas interactions

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

Roncaratti, L. F., E-mail: lz@fis.unb.br; Leal, L. A.; Silva, G. M. de

2014-10-07

We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H{sub 2}O{sub 2}−Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry ofmore » the H{sub 2}O{sub 2} molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H{sub 2}O{sub 2} molecule, or other systems involving O–O and S–S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O–H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.« less

Crystal structures of (±)-(1SR,5SR,6SR,7SR,10SR,11SR,13RS,14SR)-13-hy-droxy-7-meth-oxy-meth-oxy-11,15,18,18-tetra-methyl-3-oxo-2,4-dioxa-tetra-cyclo-[12.3.1.0(1,5).0(6,11)]octa-dec-15-en-10-yl benzoate, its 13-epimer and 13-one derivative.

PubMed

Oishi, Takeshi; Fukaya, Keisuke; Yamaguchi, Yu; Sugai, Tomoya; Watanabe, Ami; Sato, Takaaki; Chida, Noritaka

2015-05-01

The title compounds, C29H38O8·0.25C5H12, (A), C29H38O8, (B), and C29H36O8, (C), are tetra-cyclic benzoates possessing a taxane skeleton with a fused dioxolane ring as the core structure. In the asymmetric unit of (A), there are two independent benzoate mol-ecules (A and A') and a half mol-ecule of solvent pentane disordered about an inversion center. The mol-ecular conformations of (A), (B) and (C) are similar except for the flexible meth-oxy-meth-oxy group. The cyclo-hexane, cyclo-hexene and central cyclo-octane rings adopt chair, half-chair and chair-chair (extended crown) forms, respectively. The dioxolane rings are essentially planar, while the dioxolane ring of A' is slightly twisted from the mean plane. In the crystal of (A), inter-molecular O-H⋯O, C-H⋯O and C-H⋯π inter-actions link the independent benzoates alternately, forming a chain structure. In the crystals of (B) and (C), mol-ecules are linked through O-H⋯O and C-H⋯π inter-actions, and C-H⋯O hydrogen bonds, respectively, into similar chains. Further, weak inter-molecular C-H⋯O inter-actions connect the chains into a three-dimensional network in (A) and a sheet in (B), whereas no other interactions are observed for (C).

Production of low kinetic energy electrons and energetic ion pairs by Intermolecular Coulombic Decay.

PubMed

Hergenhahn, Uwe

2012-12-01

The paper gives an introduction into Interatomic and Intermolecular Coulombic Decay (ICD). ICD is an autoionization process, which contrary to Auger decay involves neighbouring sites of the initial vacancy as an integral part of the decay transition. As a result of ICD, slow electrons are produced which generally are known to be active in radiation damage. The author summarizes the properties of ICD and reviews a number of important experiments performed in recent years. Intermolecular Coulombic Decay can generally take place in weakly bonded aggregates in the presence of ionizing particles or ionizing radiation. Examples collected here mostly use soft X-rays produced by synchrotron radiation to ionize, and use rare-gas clusters, water clusters or solutes in a liquid jet to observe ICD after irradiation. Intermolecular Coulombic Decay is initiated by single ionization into an excited state. The subsequent relaxation proceeds via an ultra-fast energy transfer to a neighbouring site, where a second ionization occurs. Secondary electrons from ICD have clearly been identified in numerous systems. ICD can take place after primary ionization, as the second step of a decay cascade which also involves Auger decay, or after resonant excitation with an energy which exceeds the ionization potential of the system. ICD is expected to play a role whenever particles or radiation with photon energies above the ionization energies for inner valence electrons are present in weakly bonded matter, e.g., biological tissue. The process produces at the same time a slow electron and two charged atomic or molecular fragments, which will lead to structural changes around the ionized site.

Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

PubMed

Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

2017-05-04

Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C 1 mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast, the interaction energy between the cellulose and water is too weak to dissolve cellulose in water.

Ultraviolet photoelectron spectroscopy reveals energy-band dispersion for π-stacked 7,8,15,16-tetraazaterrylene thin films in a donor–acceptor bulk heterojunction

NASA Astrophysics Data System (ADS)

Aghdassi, Nabi; Wang, Qi; Ji, Ru-Ru; Wang, Bin; Fan, Jian; Duhm, Steffen

2018-05-01

7,8,15,16-tetraazaterrylene (TAT) thin films grown on highly oriented pyrolytic graphite (HOPG) substrates were studied extensively with regard to their intrinsic and interfacial electronic properties by means of ultraviolet photoelectron spectroscopy (UPS). Merely weak substrate–adsorbate interaction occurs at the TAT/HOPG interface, with interface energetics being only little affected by the nominal film thickness. Photon energy-dependent UPS performed perpendicular to the molecular planes of TAT multilayer films at room temperature clearly reveals band-like intermolecular dispersion of the TAT highest occupied molecular orbital (HOMO) energy. Based on a comparison with a tight-binding model, a relatively narrow bandwidth of 54 meV is derived, which points to the presence of an intermediate regime between hopping and band-like hole transport. Upon additional deposition of 2,2‧:5‧,2″:5″,2″‧-quaterthiophene (4T), a 4T:TAT donor–acceptor bulk heterojunction with a considerable HOMO-level offset at the donor–acceptor interface is formed. The 4T:TAT bulk heterojunction likewise exhibits intermolecular dispersion of the TAT HOMO energy, yet with a significant decreased bandwidth.

Ultraviolet photoelectron spectroscopy reveals energy-band dispersion for π-stacked 7,8,15,16-tetraazaterrylene thin films in a donor-acceptor bulk heterojunction.

PubMed

Aghdassi, Nabi; Wang, Qi; Ji, Ru-Ru; Wang, Bin; Fan, Jian; Duhm, Steffen

2018-05-11

7,8,15,16-tetraazaterrylene (TAT) thin films grown on highly oriented pyrolytic graphite (HOPG) substrates were studied extensively with regard to their intrinsic and interfacial electronic properties by means of ultraviolet photoelectron spectroscopy (UPS). Merely weak substrate-adsorbate interaction occurs at the TAT/HOPG interface, with interface energetics being only little affected by the nominal film thickness. Photon energy-dependent UPS performed perpendicular to the molecular planes of TAT multilayer films at room temperature clearly reveals band-like intermolecular dispersion of the TAT highest occupied molecular orbital (HOMO) energy. Based on a comparison with a tight-binding model, a relatively narrow bandwidth of 54 meV is derived, which points to the presence of an intermediate regime between hopping and band-like hole transport. Upon additional deposition of 2,2':5',2″:5″,2″'-quaterthiophene (4T), a 4T:TAT donor-acceptor bulk heterojunction with a considerable HOMO-level offset at the donor-acceptor interface is formed. The 4T:TAT bulk heterojunction likewise exhibits intermolecular dispersion of the TAT HOMO energy, yet with a significant decreased bandwidth.

Effect of carboxymethyl cellulose concentration on physical properties of biodegradable cassava starch-based films

PubMed Central

2011-01-01

Background Cassava starch, the economically important agricultural commodity in Thailand, can readily be cast into films. However, the cassava starch film is brittle and weak, leading to inadequate mechanical properties. The properties of starch film can be improved by adding plasticizers and blending with the other biopolymers. Results Cassava starch (5%w/v) based films plasticized with glycerol (30 g/100 g starch) were characterized with respect to the effect of carboxymethyl cellulose (CMC) concentrations (0, 10, 20, 30 and 40%w/w total solid) and relative humidity (34 and 54%RH) on the mechanical properties of the films. Additionally, intermolecular interactions were determined by Fourier transform infrared spectroscopy (FT-IR), melting temperature by differential scanning calorimetry (DSC), and morphology by scanning electron microscopy (SEM). Water solubility of the films was also determined. Increasing concentration of CMC increased tensile strength, reduced elongation at break, and decreased water solubility of the blended films. FT-IR spectra indicated intermolecular interactions between cassava starch and CMC in blended films by shifting of carboxyl (C = O) and OH groups. DSC thermograms and SEM micrographs confirmed homogeneity of cassava starch-CMC films. Conclusion The addition of CMC to the cassava starch films increased tensile strength and reduced elongation at break of the blended films. This was ascribed to the good interaction between cassava starch and CMC. Cassava starch-CMC composite films have the potential to replace conventional packaging, and the films developed in this work are suggested to be suitable for low moisture food and pharmaceutical products. PMID:21306655

Theoretical modeling of the electronic structure and exchange interactions in Cu(II)Pc

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.; Wang, Hai; Wu, Zhenlin; Gardener, Jules; Heutz, Sandrine; Jones, Tim; Aeppli, Gabriel

2012-12-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine (Cu(II)Pc) crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green's function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α- and β-phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Theoretical modeling of the electronic structure and exchange interactions in a Cu(II)Pc one-dimensional chain

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.

2011-07-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine [Cu(II)Pc] crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green’s function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap, and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α and β phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Molecular modeling and spectroscopic studies on the interaction of the chiral drug venlafaxine hydrochloride with bovine serum albumin

NASA Astrophysics Data System (ADS)

Shahabadi, Nahid; Hadidi, Saba

2014-03-01

This study was designed to examine the interaction of racemic antidepressant drug "S,R-venlafaxine hydrochloride (VEN)" with bovine serum albumin (BSA) under physiological conditions. The mechanism of interaction was studied by spectroscopic techniques combination with molecular modeling. Stern-Volmer analysis of fluorescence quenching data shows the presence of the static quenching mechanism. The thermodynamic parameters indicated that the hydrogen bonding and weak van der Waals interactions are the predominant intermolecular forces stabilizing the complex. The number of binding sites (n) was calculated. Through the site marker competitive experiment, VEN was confirmed to be located in subdomain IIIA of BSA. The binding distance (r = 4.93 nm) between the donor BSA and acceptor VEN was obtained according to Förster's non-radiative energy transfer theory. According to UV-vis spectra and CD data binding of VEN leaded to conformational changes of BSA. Molecular docking simulations of S and R-VEN revealed that both isomers have similar interaction and the same binding sites, from this point of view S and R isomers are equal.

Nuclear spin-lattice relaxation at field-induced level crossings in a Cr8F8 pivalate single crystal

NASA Astrophysics Data System (ADS)

Yamamoto, Shoji

2016-01-01

We construct a microscopic theory for the proton spin-lattice relaxation-rate 1 /T1 measurements around field-induced level crossings in a single crystal of the trivalent chromium ion wheel complex [Cr8F8(OOCtBu)16] at sufficiently low temperatures [E. Micotti et al., Phys. Rev. B 72 (2005) 020405(R)]. Exactly diagonalizing a well-equipped spin Hamiltonian for the individual clusters and giving further consideration to their possible interactions, we reveal the mechanism of 1 /T1 being single-peaked normally at the first level crossing but double-peaked intriguingly around the second level crossing. We wipe out the doubt about poor crystallization and find out a solution-intramolecular alternating Dzyaloshinsky-Moriya interaction combined with intermolecular coupling of antiferromagnetic character, each of which is so weak as several tens of mK in magnitude.

Role of dbnd NOH intermolecular interactions in oxime derivatives via Crystal structure, Hirshfeld surface, PIXELC and DFT calculations

NASA Astrophysics Data System (ADS)

Purushothaman, Gayathri; Thiruvenkatam, Vijay

2017-11-01

Oximes are building block of organic synthesis and they have wide range applications in laboratories, industries, and pharmaceutical as antidotes. Herein we report the crystal structures of oxime derivative Beta-p-Dimethylaminodeoxybenzionoxime (I) and o-Chloro-p-dimethylaminodeoxybenzion (II) the precursor molecule of o-Chloro-p-dimethylaminodeoxybenzionoxime and their intermolecular interactions studies through Hirshfeld surface & 2D-fingerprint plot analysis along with PIXELC and DFT calculations. The packing arrangements in I and II are driven by Osbnd H⋯N and Osbnd H⋯C interactions respectively. The Osbnd H⋯N hydrogen bonding in I facilitates the formation of the dimer with the motif of R (22(6)), whereas in II absence of oxime moiety (dbnd NOH) restricts the dimer formation. The 2D-fingerprint plot shows the close contacts for the intermolecular interactions in I & II. The PIXELC calculation of II suggests Osbnd H⋯C contributes for intermolecular interaction that stabilizes the crystal packing with the total energy value of 60.4 kcal/mol. The DFT calculation using B3LYP with 6-311G (d, p) functional set for both the derivatives shows a small deviation in the benzene ring (I) and chlorobenzene ring (II) with the RMSD value of 0.5095 Å and 0.8472 Å respectively.

Intermolecular vibrational modes and H-bond interactions in crystalline urea investigated by terahertz spectroscopy and theoretical calculation

NASA Astrophysics Data System (ADS)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Hu, Cong; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-01-01

The characteristic absorption spectra of crystalline urea in 0.6-1.8 THz region have been measured by terahertz time-domain spectroscopy at room temperature experimentally. Five broad absorption peaks were observed at 0.69, 1.08, 1.27, 1.47 and 1.64 THz respectively. Moreover, density functional theory (DFT) calculation has been performed for the isolated urea molecule, and there is no infrared intensity in the region below 1.8 THz. This means that single molecule calculations are failure to predict the experimental spectra of urea crystals. To simulate these spectra, calculations on a cluster of seven urea molecules using M06-2X and B3LYP-D3 are performed, and we found that M06-2X perform better. The observed THz vibrational modes are assigned to bending and torsional modes related to the intermolecular H-bond interactions with the help of potential energy distribution (PED) method. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular H-bond interactions in urea crystals are visualized. Therefore, we can confirm that terahertz spectroscopy can be used as an effective means to detect intermolecular H-bond interactions in molecular crystals.

Crystal structure of 1-(3-chloro-phen-yl)piperazin-1-ium picrate-picric acid (2/1).

PubMed

Kavitha, Channappa N; Jasinski, Jerry P; Kaur, Manpreet; Anderson, Brian J; Yathirajan, H S

2014-11-01

The title salt {systematic name: bis-[1-(3-chloro-phen-yl)piperazinium 2,4,6-tri-nitro-phenolate]-picric acid (2/1)}, 2C10H14ClN2 (+)·2C6H5N3O7 (-)·C6H6N3O7, crystallized with two independent 1-(3-chloro-phen-yl)piperazinium cations, two picrate anions and a picric acid mol-ecule in the asymmetric unit. The six-membered piperazine ring in each cation adopts a slightly distorted chair conformation and contains a protonated N atom. In the picric acid mol-ecule, the mean planes of the nitro groups in the ortho-, meta-, and para-positions are twisted from the benzene ring by 31.5 (3), 7.7 (1), and 3.8 (2)°, respectively. In the anions, the dihedral angles between the benzene ring and the ortho-, meta-, and para-nitro groups are 36.7 (1), 5.0 (6), 4.8 (2)°, and 34.4 (9), 15.3 (8), 4.5 (1)°, respectively. The nitro group in one anion is disordered and was modeled with two sites for one O atom with an occupancy ratio of 0.627 (7):0.373 (7). In the crystal, the picric acid mol-ecule inter-acts with the picrate anion through a trifurcated O-H⋯O four-centre hydrogen bond involving an intra-molecular O-H⋯O hydrogen bond and a weak C-H⋯O inter-action. Weak inter-molecular C-H⋯O inter-actions are responsible for the formation of cation-anion-cation trimers resulting in a chain along [010]. In addition, weak C-H⋯Cl and weak π-π inter-actions [centroid-centroid distances of 3.532 (3), 3.756 (4) and 3.705 (3) Å] are observed and contribute to the stability of the crystal packing.

Weak interactions and cooperativity effects on disiloxane: a look at the building block of silicones

NASA Astrophysics Data System (ADS)

Martín-Fernández, Carlos; Montero-Campillo, M. Merced; Alkorta, Ibon; Elguero, José

2018-06-01

The behaviour of disiloxane 1 towards a set of Lewis acids (LA) and Lewis bases (LB) forming complexes through its oxygen and silicon atoms, respectively, was studied at the MP2/aug‧-cc-pVTZ level of theory, exploring a wide variety of non-covalent interactions. Disiloxane is a moderate electron acceptor and a good electron donor, exhibiting in the latter case binding energies up to almost -100 kJ/mol with BeCl2. Cooperativity effects were also analysed by looking at ternary 1:LA:LB complexes. Shorter intermolecular distances than in the corresponding binary complexes and a negative contribution of the three-body term to the binding energy indicate that the non-covalent interactions allowed by disiloxane through its acid and basic centres cooperate between them to reinforce both donor-acceptor pairs. These effects are particularly strong in complexes involving beryllium and triel bonds, but are also relevant for complexes containing hydrogen bonds.

Molecular structures of five adducts assembled from p-dimethylaminobenzaldehyde and organic acids

NASA Astrophysics Data System (ADS)

Jin, Shouwen; Wang, Lanqing; Liu, Hui; Liu, Li; Zhang, Huan; Wang, Daqi; Li, Minghui; Guo, Jianzhong; Guo, Ming

2016-07-01

Five adducts 1-5 derived from p-dimethylaminobenzaldehyde have been prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. Of the five adducts two are organic salts (1, and 2) and the other three (3-5) are cocrystals. In salts 1, and 2, the L molecules are protonated. The supramolecular architectures of the adducts 1-5 involve extensive intermolecular N-H⋯O, O-H⋯O, O-H⋯S, and C-H⋯O hydrogen bonds as well as other non-covalent interactions. The role of weak and strong non-covalent interactions in the crystal packing is ascertained. The complexes displayed 2D/3D framework structure for the synergistic effect of the various non-covalent interactions. The results presented herein tell that the strength and directionality of the N-H⋯O, O-H⋯O, and O-H⋯S hydrogen bonds between organic acids and p-dimethylaminobenzaldehyde are sufficient to bring about the formation of binary cocrystals or organic salts.

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations.

PubMed

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-14

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-01

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

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

Brammer, L.; Mareque Rivas, J.C.; Zhao, D.

Low-temperature crystal structures of QuinH{sup +}Co(CO){sub 4}{sup {minus}}, 1 (QuinH{sup +} = quinuclidinium), (DABCO)H{sup +}Co(CO){sub 3}P-(p-tolyl){sub 3}{sup {minus}}, 2, and (DABCO)H{sup +}Co(CO){sub 3}PPh{sub 2}(p-tolyl){sup {minus}}, 3 (DABCO = 1,4-diazabicyclooctane), 2 and 3 as their acetonitrile solvates, demonstrate that these salts exhibit intermolecular N--H{hor_ellipsis}Co hydrogen bonding between the cation and anion components. NMR and IR data demonstrate the persistence of these interactions in toluene solution. Such solution-state data, which examine solvated ion pairs, suggest little difference between these salts and the corresponding previously reported salts (DABCO)H{sup +}Co(CO){sub 3}L{sup {minus}} (4, L = CO; 5, L = PPh{sub 3}). However, in themore » solid state, the N--H{hor_ellipsis}Co hydrogen bonds in 1--3 are some 0.1--0.15 {angstrom} longer than would be predicted from consideration of the structures of 4 and 5 and the aforementioned similarity to 4 and 5 in solution. In previous reports the authors have shown that major steric or electronic changes to the anion or cation have resulted in substantial changes (0.15--0.3 {angstrom}) in the N{hor_ellipsis}Co [H{hor_ellipsis}] separation for N--H{hor_ellipsis}Co hydrogen bonds in related R{sub 3}NH{sup +}Co(CO){sub 3}L{sup {minus}} (L = CO, PR{sub 3}) salts. In this report, the authors present examples in which small changes are made to the anion or cation remote from the N--H{hor_ellipsis}Co hydrogen bond. In the solid state, the effect of these small changes on this hydrogen bond is subsumed by the effect of changes in the supramolecular structure. This clearly indicates the sensitivity of the geometry of these hydrogen bonds to the overall balance of intermolecular interactions in the solid state and as such is pertinent to current interest in weak (intermolecular) interactions for which characterization by X-ray crystallography is important.« less

Intermolecular vs molecule–substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)

PubMed Central

Roos, Michael; Uhl, Benedikt; Künzel, Daniela; Hoster, Harry E; Groß, Axel

2011-01-01

Summary The competition between intermolecular interactions and long-range lateral variations in the substrate–adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moiré structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results. PMID:22003444

Intermolecular interactions and aggregation of fac-tris(2-phenylpyridinato-C2,N)iridium(III) in nonpolar solvents.

PubMed

Takayasu, Satoshi; Suzuki, Takayoshi; Shinozaki, Kazuteru

2013-08-15

The intermolecular interaction and aggregation of the neutral complex fac-tris(2-phenylpyridinato-C(2),N)iridium(III) (fac-Ir(ppy)3) in solution was investigated. Intermolecular interactions were found to effectively decrease the luminescence lifetime via self-quenching with increasing fac-Ir(ppy)3 concentrations. A Stern-Volmer plot for quenching in acetonitrile was linear, due to bimolecular self-quenching, but curved in toluene as the result of excimer formation. (1)H NMR spectra demonstrated a monomer-aggregate equilibrium which resulted in spectral shifts depending on solvent polarity. X-ray crystallography provided structural information concerning the aggregate, which is based on a tetramer consisting of two Δ-fac-Ir(ppy)3-Λ-fac-Ir(ppy)3 pairs. Offset π-π stacking of ppy ligands and electrostatic dipole-dipole interactions between complex molecules play an important role in the formation of these molecular pairs.

Controlled Self-Assembly of Low-Dimensional Alq3 Nanostructures from 1D Nanowires to 2D Plates via Intermolecular Interactions

NASA Astrophysics Data System (ADS)

Gu, Jianmin; Yin, Baipeng; Fu, Shaoyan; Jin, Cuihong; Liu, Xin; Bian, Zhenpan; Li, Jianjun; Wang, Lu; Li, Xiaoyu

2018-03-01

Due to the intense influence of the shape and size of the photon building blocks on the limitation and guidance of optical waves, an important strategy is the fabrication of different structures. Herein, organic semiconductor tris-(8-hydroxyquinoline)aluminium (Alq3) nanostructures with controllable morphology, ranging from one-dimensional nanowires to two-dimensional plates, have been prepared through altering intermolecular interactions with employing the anti-solvent diffusion cooperate with solvent-volatilization induced self-assembly method. The morphologies of the formed nanostructures, which are closely related to the stacking modes of the molecules, can be exactly controlled by altering the polarity of anti-solvents that can influence various intermolecular interactions. The synthesis strategy reported here can potentially be extended to other functional organic nanomaterials.

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

Lee, Myeong H., E-mail: myeong.lee@warwick.ac.uk; Troisi, Alessandro

Vibronic coupling between the electronic and vibrational degrees of freedom has been reported to play an important role in charge and exciton transport in organic photovoltaic materials, molecular aggregates, and light-harvesting complexes. Explicitly accounting for effective vibrational modes rather than treating them as a thermal environment has been shown to be crucial to describe the effect of vibronic coupling. We present a methodology to study dissipative quantum dynamics of vibronically coupled systems based on a surrogate Hamiltonian approach, which is in principle not limited by Markov approximation or weak system-bath interaction, using a vibronic basis. We apply vibronic surrogate Hamiltonianmore » method to a linear chain system and discuss how different types of relaxation process, intramolecular vibrational relaxation and intermolecular vibronic relaxation, influence population dynamics of dissipative vibronic systems.« less

Intermolecular Interaction between Phosphatidylcholine and Sulfobetaine Lipid: A Combination of Lipids with Antiparallel Arranged Headgroup Charge.

PubMed

Aikawa, Tatsuo; Yokota, Keisuke; Kondo, Takeshi; Yuasa, Makoto

2016-10-05

Intermolecular interactions between lipid molecules are important when designing lipid bilayer interfaces, which have many biomedical applications such as in drug delivery vehicles and biosensors. Phosphatidylcholine, a naturally occurring lipid, is the most common lipid found in organisms. Its chemical structure has a negatively charged phosphate linkage, adjacent to an ester linkage in a glycerol moiety, and a positively charged choline group, placed at the terminus of the molecule. Recently, several types of synthetic lipids that have headgroups with the opposite charge to that of phosphatidylcholine have emerged; that is, a positively charged ammonium group is present adjacent to the ester linkage in their glycerol moiety and a negatively charged group is placed at their terminus. These types of lipids constitute a new class of soft material. The aim of this study was to determine how such lipids, with antiparallel arranged headgroup charge, interact with naturally occurring phosphatidylcholines. We synthesized 1,2-dipalmitoyl-sn-glycero-3-sulfobetaine (DPSB) to represent a reversed-head lipid; 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was used to represent a naturally occurring phospholipid. The intermolecular interaction between these lipids was investigated using surface pressure-area (π-A) isotherms of the lipid monolayer at the air/water interface. We found that the extrapolated area and excess free energy of the mixed monolayer deviated negatively when compared with the ideal values from additivity. Moreover, differential scanning calorimetry of the lipid mixture in aqueous dispersion showed that the gel-to-liquid crystal transition temperature increased compared with that of each pure lipid composition. These results clearly indicate that DPSB preferably interacts with DPPC in the mixture. We believe that the attraction between the oppositely charged headgroups of these lipids reinforces the intermolecular interaction. Our results provide insight into the intermolecular interaction between phospholipids and reversed-head lipids, which may prove useful for the design of lipid-based materials in the future.

Synthesis, crystal structures, and optical properties of the π-π interacting pyrrolo[2,3-b]quinoxaline derivatives containing 2-thienyl substituent

NASA Astrophysics Data System (ADS)

Goszczycki, Piotr; Stadnicka, Katarzyna; Brela, Mateusz Z.; Grolik, Jarosław; Ostrowska, Katarzyna

2017-10-01

Three (E/Z)-diastereoisomers, based on pyrrolo[2,3-b]quinoxaline system as fluorophore and containing: 2-thienylmethyl (1), bis(2-thienylmethyl)-2-aminoethyl (3a), bis(2-thienylmethyl)-3-aminopropyl (3b) groups as substituents, were synthesized and characterized by X-ray structural analysis, PXRD, NMR, UV-Vis as well as fluorescence. These compounds are non-fluorescent in acetonitrile solution, however, they exhibit aggregation induced emission enhancement (AIEE) upon water addition and in solid state. X-ray structural analysis revealed that molecules with 2-thienylmethyl and bis(2-thienylmethyl)-2-aminoethyl groups form dimers and π-stacks through π-π interactions between anitiparallel oriented pyrroloquinoxaline cores with interplanar distances 3.45 Å and 3.20 Å, respectively. Conformation of bis(2-thienylmethyl)-3-aminopropyl group is imposed by incorporated DMSO-d6 solvent molecule and weak intermolecular S-π and CH-π interactions, that prevents π-π interaction between fluorophore cores. The correlation between crystal structure and fluorescent properties of synthesized molecules was discussed. The DFT calculations were performed to rationalize the differences between considered systems.

Positronium formation studies in crystalline molecular complexes: Triphenylphosphine oxide - Acetanilide

NASA Astrophysics Data System (ADS)

Oliveira, F. C.; Denadai, A. M. L.; Guerra, L. D. L.; Fulgêncio, F. H.; Windmöller, D.; Santos, G. C.; Fernandes, N. G.; Yoshida, M. I.; Donnici, C. L.; Magalhães, W. F.; Machado, J. C.

2013-04-01

Hydrogen bond formation in the triphenylphosphine oxide (TPPO), acetanilide (ACN) supramolecular heterosynton system, named [TPPO0.5·ACN0.5], has been studied by Positron Annihilation Lifetime Spectroscopy (PALS) and supported by several analytical techniques. In toluene solution, Isothermal Titration Calorimetry (ITC) presented a 1:1 stoichiometry and indicated that the complexation process is driven by entropy, with low enthalpy contribution. X-ray structure determination showed the existence of a three-dimensional network of hydrogen bonds, allowing also the confirmation of the existence of a 1:1 crystalline molecular complex in solid state. The results of thermal analysis (TGA, DTA and DSC) and FTIR spectroscopy showed that the interactions in the complex are relatively weaker than those found in pure precursors, leading to a higher positronium formation probability at [TPPO0.5·ACN0.5]. These weak interactions in the complex enhance the possibility of the n- and π-electrons to interact with positrons and consequently, the probability of positronium formation is higher. Through the present work is shown that PALS is a sensible powerful tool to investigate intermolecular interactions in solid heterosynton supramolecular systems.

Cooperative and diminutive unusual weak bonding in F3CX···HMgH···Y and F3CX···Y···HMgH trimers (X = Cl, Br; Y = HCN, and HNC).

PubMed

Solimannejad, Mohammad; Malekani, Masumeh; Alkorta, Ibon

2010-11-18

MP2 calculations with cc-pVTZ basis set were used to analyze intermolecular interactions in F(3)CX···HMgH···Y and F(3)CX···Y···HMgH triads (X = Cl, Br; Y = HCN, and HNC) which are connecting with three kinds of unusual weak interactions, namely halogen-hydride, dihydrogen, and σ-hole. To understand the properties of the systems better, the corresponding dyads are also studied. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads were investigated at the MP2/cc-pVTZ computational level. Particular attention is given to parameters such as cooperative energies, cooperative dipole moments, and many-body interaction energies. Those complexes with simultaneous presence of a σ-hole bond and a dihydrogen bond show cooperativity energy ranging between -1.02 and -2.31 kJ mol(-1), whereas those with a halogen-hydride bond and a dihydrogen bond are diminutive, with this energetic effect between 0.1 and 0.63 kJ mol(-1). The electronic properties of the complexes have been analyzed using the molecular electrostatic potential (MEP), the electron density shift maps, and the parameters derived from the atoms in molecules (AIM) methodology.

Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing.

PubMed

Patil, Rohan; Das, Suranjana; Stanley, Ashley; Yadav, Lumbani; Sudhakar, Akulapalli; Varma, Ashok K

2010-08-16

Weak intermolecular interactions such as hydrogen bonding and hydrophobic interactions are key players in stabilizing energetically-favored ligands, in an open conformational environment of protein structures. However, it is still poorly understood how the binding parameters associated with these interactions facilitate a drug-lead to recognize a specific target and improve drugs efficacy. To understand this, comprehensive analysis of hydrophobic interactions, hydrogen bonding and binding affinity have been analyzed at the interface of c-Src and c-Abl kinases and 4-amino substituted 1H-pyrazolo [3, 4-d] pyrimidine compounds. In-silico docking studies were performed, using Discovery Studio software modules LigandFit, CDOCKER and ZDOCK, to investigate the role of ligand binding affinity at the hydrophobic pocket of c-Src and c-Abl kinase. Hydrophobic and hydrogen bonding interactions of docked molecules were compared using LigPlot program. Furthermore, 3D-QSAR and MFA calculations were scrutinized to quantify the role of weak interactions in binding affinity and drug efficacy. The in-silico method has enabled us to reveal that a multi-targeted small molecule binds with low affinity to its respective targets. But its binding affinity can be altered by integrating the conformationally favored functional groups at the active site of the ligand-target interface. Docking studies of 4-amino-substituted molecules at the bioactive cascade of the c-Src and c-Abl have concluded that 3D structural folding at the protein-ligand groove is also a hallmark for molecular recognition of multi-targeted compounds and for predicting their biological activity. The results presented here demonstrate that hydrogen bonding and optimized hydrophobic interactions both stabilize the ligands at the target site, and help alter binding affinity and drug efficacy.

Optimized Hydrophobic Interactions and Hydrogen Bonding at the Target-Ligand Interface Leads the Pathways of Drug-Designing

PubMed Central

Stanley, Ashley; Yadav, Lumbani; Sudhakar, Akulapalli; Varma, Ashok K.

2010-01-01

Background Weak intermolecular interactions such as hydrogen bonding and hydrophobic interactions are key players in stabilizing energetically-favored ligands, in an open conformational environment of protein structures. However, it is still poorly understood how the binding parameters associated with these interactions facilitate a drug-lead to recognize a specific target and improve drugs efficacy. To understand this, comprehensive analysis of hydrophobic interactions, hydrogen bonding and binding affinity have been analyzed at the interface of c-Src and c-Abl kinases and 4-amino substituted 1H-pyrazolo [3, 4-d] pyrimidine compounds. Methodology In-silico docking studies were performed, using Discovery Studio software modules LigandFit, CDOCKER and ZDOCK, to investigate the role of ligand binding affinity at the hydrophobic pocket of c-Src and c-Abl kinase. Hydrophobic and hydrogen bonding interactions of docked molecules were compared using LigPlot program. Furthermore, 3D-QSAR and MFA calculations were scrutinized to quantify the role of weak interactions in binding affinity and drug efficacy. Conclusions The in-silico method has enabled us to reveal that a multi-targeted small molecule binds with low affinity to its respective targets. But its binding affinity can be altered by integrating the conformationally favored functional groups at the active site of the ligand-target interface. Docking studies of 4-amino-substituted molecules at the bioactive cascade of the c-Src and c-Abl have concluded that 3D structural folding at the protein-ligand groove is also a hallmark for molecular recognition of multi-targeted compounds and for predicting their biological activity. The results presented here demonstrate that hydrogen bonding and optimized hydrophobic interactions both stabilize the ligands at the target site, and help alter binding affinity and drug efficacy. PMID:20808434

Interplay of intermolecular interactions and flexibility to mediate glass forming ability and fragility: A study of chemical analogs

NASA Astrophysics Data System (ADS)

Saini, Manoj K.; Jin, Xiao; Wu, Tao; Liu, Yingdan; Wang, Li-Min

2018-03-01

We have investigated the enthalpic and dielectric relaxations of four groups of quinoline analogs having similar structural properties (i.e., rigidity, stiffness, and bulkiness) but a different steric character and the nature of intermolecular interactions and flexibility. The dielectric fragility index (md) and the enthalpic one (mH), determined by the Tool-Narayanaswamy-Moynihan-Hodge formalism, are comparable. Generally, for the four sets of molecules of similar structures, both the interactions and flexibility are found to be critical in making the large span of fragility (i.e., from 59 to 131) and glass forming ability. By contrast, individual impacts of the interaction and flexibility can only explain fragility partly among each group of isomers. We found that the molecules with high fragility are of relatively low liquid density, reflecting the joint impact of the interactions and flexibility. An interesting result is observed among the isomers that the molecules which are fragile have enhanced glass forming ability. The results are unveiling the joint impacts of molecular structure (flexibility) and intermolecular interaction on the molecular dynamics.

Concerted Mitigation of O···H and C(π)···H Interactions Prospects Sixfold Gain in Optical Nonlinearity of Ionic Stilbazolium Derivatives

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

Cole, Jacqueline M.; Lin, Tze-Chia; Edwards, Alison J.

2015-03-04

DAST (4-dimethylamino-N-methyl-4-stilbazolium tosylate) is the most commercially successful organic nonlinear optical (NLO) material for frequency-doubling, integrated optics, and THz wave applications. Its success is predicated on its high optical nonlinearity with concurrent sufficient thermal stability. Many chemical derivatives of DAST have therefore been developed to optimize their properties; yet, to date, none have surpassed the overall superiority of DAST for NLO photonic applications. This is perhaps because DAST is an ionic salt wherein its NLO-active cation is influenced by multiple types of subtle intermolecular forces that are hard to quantify, thus, making difficult the molecular engineering of better functioning DASTmore » derivatives. Here, we establish a model parameter, ηinter, that isolates the influence of intermolecular interactions on second-order optical nonlinearity in DAST and its derivatives, using second-harmonic generation (SHG) as a qualifier; by systematically mapping intercorrelations of all possible pairs of intermolecular interactions to ηinter, we uncover a relationship between concerted intermolecular interactions and SHG output. This correlation reveals that a sixfold gain in the intrinsic second-order NLO performance of DAST is possible, by eliminating the identified interactions. This prediction offers the first opportunity to systematically design next-generation DAST-based photonic device nanotechnology to realize such a prospect.« less

Design of a New Concentration Series for the Orthogonal Sample Design Approach and Estimation of the Number of Reactions in Chemical Systems.

PubMed

Shi, Jiajia; Liu, Yuhai; Guo, Ran; Li, Xiaopei; He, Anqi; Gao, Yunlong; Wei, Yongju; Liu, Cuige; Zhao, Ying; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

2015-11-01

A new concentration series is proposed for the construction of a two-dimensional (2D) synchronous spectrum for orthogonal sample design analysis to probe intermolecular interaction between solutes dissolved in the same solutions. The obtained 2D synchronous spectrum possesses the following two properties: (1) cross peaks in the 2D synchronous spectra can be used to reflect intermolecular interaction reliably, since interference portions that have nothing to do with intermolecular interaction are completely removed, and (2) the two-dimensional synchronous spectrum produced can effectively avoid accidental collinearity. Hence, the correct number of nonzero eigenvalues can be obtained so that the number of chemical reactions can be estimated. In a real chemical system, noise present in one-dimensional spectra may also produce nonzero eigenvalues. To get the correct number of chemical reactions, we classified nonzero eigenvalues into significant nonzero eigenvalues and insignificant nonzero eigenvalues. Significant nonzero eigenvalues can be identified by inspecting the pattern of the corresponding eigenvector with help of the Durbin-Watson statistic. As a result, the correct number of chemical reactions can be obtained from significant nonzero eigenvalues. This approach provides a solid basis to obtain insight into subtle spectral variations caused by intermolecular interaction.

Synthesis, crystal structure, spectroscopic characterization, docking simulation and density functional studies of 1-(3,4-dimethoxyphenyl) -3-(4-flurophenyl)-propan-1-one

NASA Astrophysics Data System (ADS)

Khamees, Hussien Ahmed; Jyothi, Mahima; Khanum, Shaukath Ara; Madegowda, Mahendra

2018-06-01

The compound 1-(3,4-dimethoxyphenyl)-3-(4-flurophenyl)-propan-1-one (DFPO) was synthesized by Claisen-Schmidt condensation reaction and the single crystals were obtained by slow evaporation method. Three-dimensional structure was confirmed by single crystal X-ray diffraction method and exhibiting the triclinic crystal system with space group P-1. The crystal structure is stabilized by Csbnd H⋯O intermolecular and weak interactions. Computed molecular geometry has been obtained by density functional theory (DFT) and compared with experimental results. The spectra of both FT-IR in the range (4000-400 cm-1) and FT- Raman (3500-50 cm-1) of DFPO were recorded experimentally and computed by (DFT) using B3LYP/6-311G (d,p) as basis sets. Intramolecular charge transfer has been scanned using natural bond orbital (NBO) analysis and revealed the various contribution of bonding and lone pair to the stabilization of molecule. Nonlinear optical activity (NLO) of the title compound has been determined by second harmonic generation (SHG) and computed using DFT method. Hyperpolarizability, HOMO-LUMO energy gap, hardness, softness electronegativity and others Global reactivity descriptors of DFPO has been calculated and revealed complete picture of chemical reactivity of DFPO. Hirshfeld surface analyses were applied to investigate the intermolecular interactions and revealed that more than two-thirds of the inter contacts are associated with O⋯H, C⋯H and H⋯H interactions. Docking studies of DFPO showed inhibition of Vascular endothelial growth Factor human receptor (VEGFR-2) signalling pathway, which indicates DFPO as anti-angiogenesis, that play pivotal role in cancer, so we suggest it for clinical studies to evaluate its potential to treat human cancers.

Host-guest complex of N-(2-chloroethyl), N-nitroso, N‧, N‧ -dicyclohexylsulfamid with β-cyclodextrin: Fluorescence, QTAIM analysis and structure-chemical reactivity

NASA Astrophysics Data System (ADS)

Bensouilah, Nadjia; Fisli, Hassina; Bensouilah, Hamza; Zaater, Sihem; Abdaoui, Mohamed; Boutemeur-Kheddis, Baya

2017-10-01

In this work, the inclusion complex of DCY/CENS: N-(2-chloroethyl), N-nitroso, N‧, N‧-dicyclohexylsulfamid and β-cyclodextrin (β-CD) is investigated using the fluorescence spectroscopy, PM3, ONIOM2 and DFT methods. The experimental part reveals that DCY/CENS forms a 1:1 stoichiometric ratio inclusion complex with β-CD. The constant of stability is evaluated using the Benesi-Hildebrand equation. The results of the theoretical optimization showed that the lipophilic fraction of molecule (cyclohexyl group) is inside of β-CD. Accordingly, the Nitroso-Chloroethyl moiety is situated outside the cavity of the macromolecule host. The favorable structure of the optimized complex indicates the existence of weak intermolecular hydrogen bonds and the most important van der Waals (vdW) interactions which are studied on the basis of Natural Bonding Orbital (NBO) analysis. The NBO is employed to compute the electronic donor-acceptor exchanges between drug and β-CD. Furthermore, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM), has been accomplished on the most favorable complex using B3LYP/6-31G(d) method. The presence of stabilizing intermolecular hydrogen bonds and van der Waals interactions in the most favorable complex is predicted. Also, the energies of these interactions are estimated with Espinosa's formula. The findings of this investigation reveal that the correlation between the structural parameters and the electronic density is good. Finally, and based on DFT calculations, the reactivity of the interesting molecule in free state was studied and compared with that in the complexed state using chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors.

Matrix-isolation studies on the radiation-induced chemistry in H₂O/CO₂ systems: reactions of oxygen atoms and formation of HOCO radical.

PubMed

Ryazantsev, Sergey V; Feldman, Vladimir I

2015-03-19

The radiation-induced transformations occurring upon X-ray irradiation of solid CO2/H2O/Ng systems (Ng = Ar, Kr, Xe) at 8-10 K and subsequent annealing up to 45 K were studied by Fourier transform infrared spectroscopy. The infrared (IR) spectra of deposited matrices revealed the presence of isolated monomers, dimers, and intermolecular H2O···CO2 complexes. Irradiation resulted in effective decomposition of matrix-isolated carbon dioxide and water yielding CO molecules and OH radicals, respectively. Annealing of the irradiated samples led to formation of O3, HO2, and a number of xenon hydrides of HXeY type (in the case of xenon matrices). The formation of these species was used for monitoring of the postirradiation thermally induced chemical reactions involving O and H atoms generated by radiolysis. It was shown that the radiolysis of CO2 in noble-gas matrices produced high yields of stabilized oxygen atoms. In all cases, the temperatures at which O atoms become mobile and react are lower than those of H atoms. Dynamics and reactivity of oxygen atoms was found to be independent of the precursor nature. In addition, the formation of HOCO radicals was observed in all the noble-gas matrices at remarkably low temperatures. The IR spectra of HOCO and DOCO were first characterized in krypton and xenon matrices. It was concluded that the formation of HOCO was mainly due to the radiation-induced evolution of the weakly bound H2O···CO2 complexes. This result indicates the significance of weak intermolecular interactions in the radiation-induced chemical processes in inert low-temperature media.

Solvent empirical scales and their importance for the study of intermolecular interactions

NASA Astrophysics Data System (ADS)

Babusca, Daniela; Benchea, Andreea Celia; Morosanu, Ana Cezarina; Dimitriu, Dan Gheorghe; Dorohoi, Dana Ortansa

2017-01-01

The solvent empirical scales were developed in order to classify the solvents regarding their influence on the absorption or fluorescence spectra of different spectrally active molecules. The intermolecular interactions in binary solutions of three molecule having an intramolecular charge transfer visible absorption band are studied in this paper: 5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophene-2-carbaldehyde (QTC), 1-cyano-2-{5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophen-2-yl}-vinyl)-phosphonic acid diethyl ester (QTCP) and p-phenyl pyridazinium-p-nitro-phenacylid (PPNP). The solvent empirical scales with a single parameter (Z scale of Kosower, ET (30) or ETN scale of Reichardt and Dimroth) can be used to describe the strength of intermolecular interactions. The contributions of each type of interactions to the total spectral shift are evaluated using the solvent multiple parameters empirical scales defined by Kamlet and Taft and by Catalan et al.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Pharmaceutical cocrystals, salts and multicomponent systems; intermolecular interactions and property based design.

PubMed

Berry, David J; Steed, Jonathan W

2017-08-01

As small molecule drugs become harder to develop and less cost effective for patient use, efficient strategies for their property improvement become increasingly important to global health initiatives. Improvements in the physical properties of Active Pharmaceutical Ingredients (APIs), without changes in the covalent chemistry, have long been possible through the application of binary component solids. This was first achieved through the use of pharmaceutical salts, within the last 10-15years with cocrystals and more recently coamorphous systems have also been consciously applied to this problem. In order to rationally discover the best multicomponent phase for drug development, intermolecular interactions need to be considered at all stages of the process. This review highlights the current thinking in this area and the state of the art in: pharmaceutical multicomponent phase design, the intermolecular interactions in these phases, the implications of these interactions on the material properties and the pharmacokinetics in a patient. Copyright © 2017 Elsevier B.V. All rights reserved.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

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

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

A detailed study of intermolecular interactions, electronic and vibrational properties of the metal complex bis(uracilato)diammine copper(ii) dihydrate

NASA Astrophysics Data System (ADS)

Gramajo Feijoo, M.; Fernández-Liencres, M. P.; Gil, D. M.; Gómez, M. I.; Ben Altabef, A.; Navarro, A.; Tuttolomondo, M. E.

2018-03-01

Density Functional Theory (DFT) calculations were performed with the aim of investigating the vibrational, electronic and structural properties of [Cu(uracilato-N1)2 (NH3)2]ṡ2H2O complex. The IR and Raman spectra were recorded leading to a complete analysis of the normal modes of vibration of the metal complex. A careful study of the intermolecular interactions observed in solid state was performed by using the Hirshfeld surface analysis and their associated 2D fingerprint plots. The results indicated that the crystal packing is stabilized by Nsbnd H⋯O hydrogen bonds and π-stacking interactions. In addition, Csbnd H···π interactions were also observed. Time-dependent density functional theory (TD-DFT) calculations revealed that all the low-lying electronic states correspond to a mixture of intraligand charge transfer (ILCT) and ligand-to-metal charge transfer (LMCT) transitions. Finally, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) analysis were performed to shed light on the intermolecular interactions in the coordination sphere.

Universality away from critical points in a thermostatistical model

NASA Astrophysics Data System (ADS)

Lapilli, C. M.; Wexler, C.; Pfeifer, P.

Nature uses phase transitions as powerful regulators of processes ranging from climate to the alteration of phase behavior of cell membranes to protect cells from cold, building on the fact that thermodynamic properties of a solid, liquid, or gas are sensitive fingerprints of intermolecular interactions. The only known exceptions from this sensitivity are critical points. At a critical point, two phases become indistinguishable and thermodynamic properties exhibit universal behavior: systems with widely different intermolecular interactions behave identically. Here we report a major counterexample. We show that different members of a family of two-dimensional systems —the discrete p-state clock model— with different Hamiltonians describing different microscopic interactions between molecules or spins, may exhibit identical thermodynamic behavior over a wide range of temperatures. The results generate a comprehensive map of the phase diagram of the model and, by virtue of the discrete rotors behaving like continuous rotors, an emergent symmetry, not present in the Hamiltonian. This symmetry, or many-to-one map of intermolecular interactions onto thermodynamic states, demonstrates previously unknown limits for macroscopic distinguishability of different microscopic interactions.

Quantifying stickiness: thermodynamic characterization of intramolecular domain interactions to guide the design of förster resonance energy transfer sensors.

PubMed

Lindenburg, Laurens H; Malisauskas, Mantas; Sips, Tari; van Oppen, Lisanne; Wijnands, Sjors P W; van de Graaf, Stan F J; Merkx, Maarten

2014-10-14

The introduction of weak, hydrophobic interactions between fluorescent protein domains (FPs) can substantially increase the dynamic range (DR) of Förster resonance energy transfer (FRET)-based sensor systems. Here we report a comprehensive thermodynamic characterization of the stability of a range of self-associating FRET pairs. A new method is introduced that allows direct quantification of the stability of weak FP interactions by monitoring intramolecular complex formation as a function of urea concentration. The commonly used S208F mutation stabilized intramolecular FP complex formation by 2.0 kCal/mol when studied in an enhanced cyan FP (ECFP)-linker-enhanced yellow FP (EYFP) fusion protein, whereas a significantly weaker interaction was observed for the homologous Cerulean/Citrine FRET pair (ΔG0(o-c) = 0.62 kCal/mol). The latter effect could be attributed to two mutations in Cerulean (Y145A and H148D) that destabilize complex formation with Citrine. Systematic analysis of the contribution of residues 125 and 127 at the dimerization interface in mOrange.linker.mCherry fusion proteins yielded a toolbox of new mOrange-mCherry combinations that allowed tuning of their intramolecular interaction from very weak (ΔG0(o-c) = .0.39 kCal/mol) to relatively stable (ΔG0(o-c) = 2.2 kCal/mol). The effects of these mutations were also studied by monitoring homodimerization of mCherry variants using fluorescence anisotropy. These mutations affected intramolecular and intermolecular domain interactions similarly, although FP interactions were found to be stronger in the latter. The knowledge thus obtained allowed successful construction of a red-shifted variant of the bile acid FRET sensor BAS-1 by replacement of the self-associating Cerulean-Citrine pair by mOrange.mCherry variants with a similar intramolecular affinity. Our findings thus allow a better understanding of the subtle but important role of intramolecular domain interactions in current FRET sensors and help guide the construction of new sensors using modular design strategies.

Methyl 2-methyl-4-(oxiran-2-ylmeth-oxy)-2H-1,2-benzothia-zine-3-carboxyl-ate 1,1-dioxide.

PubMed

Ahmad, Matloob; Siddiqui, Hamid Latif; Zia-Ur-Rehman, Muhammad; Elsegood, Mark R J; Weaver, George W

2010-01-09

In the title compound, C(14)H(15)NO(6)S, the thia-zine ring adopts a distorted half-chair conformation. The structure displays several cooperative weak inter-molecular C-H⋯O hydrogen-bonding inter-actions, giving rise to a two-dimensional sheet packing motif. The CH(2) group in the meth-oxy linker to the oxirane ring, and the CH group in that ring, exhibit twofold positional disorder. The three-membered oxirane ring is twisted approximately perpendicular with respect to thia-zine ring (dihedral angle = 60/86° for the major/minor disorder components). 1,2-Benzothia-zines of this kind have a wide range of biological activities and are mainly used as medicines in the treatment of inflammation and rheumatoid arthritis.

Fluorescence Correlation Spectroscopy to Study Diffusion of Polymer Chains within Layered Hydrogen-Bonded Polymer Films

NASA Astrophysics Data System (ADS)

Pristinski, Denis; Kharlampieva, Evguenia; Sukhishvili, Svetlana

2002-03-01

Fluorescence Correlation Spectroscopy (FCS) has been used to probe molecular motions within polymer multilayers formed by hydrogen-bonding sequential self-assembly. Polyethylene glycol (PEG) molecules were end-labeled with the fluorescent tags, and self-assembled with polymethacrylic acid (PMAA) using layer-by-layer deposition. We have found that molecules included in the top adsorbed layer have significant mobility at the millisecond time scale, probably due to translational diffusion. However, their dynamics deviate from classical Brownian motion with a single diffusion time. Possible reasons for the deviation are discussed. We found that motions were significantly slowed with increasing depth within the PEG/PMAA multilayer. This phenomena occured in a narrow pH range around 4.0 in which intermolecular interactions were relatively weak.

Phosphine-substrate recognition through the C-H...O hydrogen bond: application to the asymmetric Pauson-Khand reaction.

PubMed

Solà, Jordi; Riera, Antoni; Verdaguer, Xavier; Maestro, Miguel A

2005-10-05

A unique methine moiety attached to three heteroatoms (O, P, S) and contained in the PuPHOS and CamPHOS ligands serves as a strong hydrogen-bond donor. Nonclassical hydrogen bonding of this methine with an amido-carbonyl acceptor provides a completely diastereoselective ligand exchange process between an alkyne dicobalthexacarbonyl complex and a phosphine ligand. This weak contact has been studied by means of X-ray analysis, 1H NMR, and quantum mechanical calculations and revealed that the present interaction falls in the range of strong C-H...O=C bonds. The hydrogen-bond bias obtained in the ligand exchange process has been exploited in the asymmetric intermolecular Pauson-Khand reaction to yield the corresponding cyclization adducts in up to 94% ee.

Chiral self-recognition: direct spectroscopic detection of the homochiral and heterochiral dimers of propylene oxide in the gas phase.

PubMed

Su, Zheng; Borho, Nicole; Xu, Yunjie

2006-12-27

In this report, we describe rotational spectroscopic and high-level ab initio studies of the 1:1 chiral molecular adduct of propylene oxide dimer. The complexes are bound by weak secondary hydrogen bonds, that is, the O(epoxy)...H-C noncovalent interactions. Six homochiral and six heterochiral conformers were predicted to be the most stable configurations where each monomer acts as a proton acceptor and a donor simultaneously, forming two six- or five-membered intermolecular hydrogen-bonded rings. Rotational spectra of six, that is, three homochiral and heterochiral conformer pairs, out of the eight conformers that were predicted to have sufficiently large permanent electric dipole moments were measured and analyzed. The relative conformational stability order and the signs of the chiral recognition energies of the six conformers were determined experimentally and were compared to the ab initio computational results. The experimental observations and the ab initio calculations suggest that the concerted effort of these weak secondary hydrogen bonds can successfully lock the subunits in a particular orientation and that the overall binding strength is comparable to a classic hydrogen bond.

Interaction between polymer constituents and the structure of biopolymers

NASA Technical Reports Server (NTRS)

Rein, R.

1974-01-01

The paper reviews the current status of methods for calculating intermolecular interactions between biopolymer units. The nature of forces contributing to the various domains of intermolecular separations is investigated, and various approximations applicable in the respective regions are examined. The predictive value of current theory is tested by establishing a connection with macroscopic properties and comparing the theoretical predicted values with those derived from experimental data. This has led to the introduction of a statistical model describing DNA.

Singlet Fission via an Excimer-Like Intermediate in 3,6-Bis(thiophen-2-yl)diketopyrrolopyrrole Derivatives.

PubMed

Mauck, Catherine M; Hartnett, Patrick E; Margulies, Eric A; Ma, Lin; Miller, Claire E; Schatz, George C; Marks, Tobin J; Wasielewski, Michael R

2016-09-14

Singlet fission (SF) in polycrystalline thin films of four 3,6-bis(thiophen-2-yl)diketopyrrolopyrrole (TDPP) chromophores with methyl (Me), n-hexyl (C6), triethylene glycol (TEG), and 2-ethylhexyl (EH) substituents at the 2,5-positions is found to involve an intermediate excimer-like state. The four different substituents yield four distinct intermolecular packing geometries, resulting in variable intermolecular charge transfer (CT) interactions in the solid. SF from the excimer state of Me, C6, TEG, and EH takes place in τSF = 22, 336, 195, and 1200 ps, respectively, to give triplet yields of 200%, 110%, 110%, and 70%, respectively. The transient spectra of the excimer-like state and its energetic proximity to the lowest excited singlet state in these derivatives suggests that this state may be the multiexciton (1)(T1T1) state that precedes formation of the uncorrelated triplet excitons. The excimer decay rates correlate well with the SF efficiencies and the degree of intermolecular donor-acceptor interactions resulting from π-stacking of the thiophene donor of one molecule with the DPP core acceptor in another molecule as observed in the crystal structures. Such interactions are found to also increase with the SF coupling energies, as calculated for each derivative. These structural and spectroscopic studies afford a better understanding of the electronic interactions that enhance SF in chromophores having strong intra- and intermolecular CT character.

Programmable display of DNA-protein chimeras for controlling cell-hydrogel interactions via reversible intermolecular hybridization.

PubMed

Zhang, Zhaoyang; Li, Shihui; Chen, Niancao; Yang, Cheng; Wang, Yong

2013-04-08

Extensive studies have been recently carried out to achieve dynamic control of cell-material interactions primarily through physicochemical stimulation. The purpose of this study was to apply reversible intermolecular hybridization to program cell-hydrogel interactions in physiological conditions based on DNA-antibody chimeras and complementary oligonucleotides. The results showed that DNA oligonucleotides could be captured to and released from the immobilizing DNA-functionalized hydrogels with high specificity via DNA hybridization. Accordingly, DNA-antibody chimeras were captured to the hydrogels, successfully inducing specific cell attachment. The cell attachment to the hydrogels reached the plateau at approximately half an hour after the functionalized hydrogels and the cells were incubated together. The attached cells were rapidly released from the bound hydrogels when triggering complementary oligonucleotides were introduced to the system. However, the capability of the triggering complementary oligonucleotides in releasing cells was affected by the length of intermolecular hybridization. The length needed to be at least more than 20 base pairs in the current experimental setting. Notably, because the procedure of intermolecular hybridization did not involve any harsh condition, the released cells maintained the same viability as that of the cultured cells. The functionalized hydrogels also exhibited the potential to catch and release cells repeatedly. Therefore, this study demonstrates that it is promising to regulate cell-material interactions dynamically through the DNA-programmed display of DNA-protein chimeras.

Photophysics of detection of explosive vapours via luminescence quenching of thin films: impact of inter-molecular interactions.

PubMed

Shoaee, Safa; Fan, Shengqiang; Burn, Paul L; Shaw, Paul E

2016-09-21

Fluorescence-based detection of explosive analytes requires an understanding of the nature of the excited state responsible for the luminescence response of a sensing material. Many measurements are carried out to elucidate the fundamental photophysical properties of an emissive material in solution. However, simple transfer of the understanding gained from the solution measurements to the solid-state can lead to errors. This is in part due to the absence of inter-molecular interactions of the chromophores in solution, which are present in the solid-state. To understand the role of inter-molecular interactions on the detection of explosive analytes we have chosen dendrimers from two different families, D1 and D2, which allow facile control of the inter-molecular interactions through the choice of dendrons and emissive chromophores. Using ultrafast transient absorption spectroscopy we find that the solution photoinduced absorption (PA) for both materials can be explained in terms of the generation of singlet excitons, which decay to the ground state, or intersystem cross (ISC) to form a triplet exciton. In neat films however, we observe different photophysical behaviours; first, ISC to the triplet state does not occur, and second, depending on the chromophore, charge transfer and charge separated states are formed. Furthermore, we find that when either dendrimer is interfaced with analyte vapour, the singlet state is strongly quenched, generating a charge transfer state that undergoes geminate recombination.

Long range intermolecular interactions between the alkali diatomics Na2, K2, and NaK

NASA Astrophysics Data System (ADS)

Zemke, Warren T.; Byrd, Jason N.; Michels, H. Harvey; Montgomery, John A.; Stwalley, William C.

2010-06-01

Long range interactions between the ground state alkali diatomics Na2-Na2, K2-K2, Na2-K2, and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential ELR=Eelec+Edisp+Eind is shown to accurately represent the intermolecular interactions for these systems at long range.

Long range intermolecular interactions between the alkali diatomics Na(2), K(2), and NaK.

PubMed

Zemke, Warren T; Byrd, Jason N; Michels, H Harvey; Montgomery, John A; Stwalley, William C

2010-06-28

Long range interactions between the ground state alkali diatomics Na(2)-Na(2), K(2)-K(2), Na(2)-K(2), and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential E(LR)=E(elec)+E(disp)+E(ind) is shown to accurately represent the intermolecular interactions for these systems at long range.

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer.

PubMed

Li, Jinshan; Zhao, Feng; Jing, Fuqian

2003-02-01

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 345-352, 2003

Matrix Isolation and ab initio study of the noncovalent complexes between formamide and acetylene.

PubMed

Mardyukov, Artur; Sánchez-García, Elsa; Sander, Wolfram

2009-02-12

Matrix isolation spectroscopy in combination with ab initio calculations is a powerful technique for the identification of weakly bound intermolecular complexes. Here, weak complexes between formamide and acetylene are studied, and three 1:1 complexes with binding energies of -2.96, -2.46, and -1.79 kcal/mol have been found at the MP2 level of theory (MP2/cc-pVTZ + ZPE + BSSE). The two most stable dimers A and B are identified in argon and nitrogen matrices by comparison between the experimental and calculated infrared frequencies. Both complexes are stabilized by the formamide C=O...HC acetylene and H...pi interactions. Large shifts have been observed experimentally for the C-H stretching vibrations of the acetylene molecule, in very good agreement with the calculated values. Eight 1:2 FMA-acetylene trimers (T-A to T-H) with binding energies between -5.44 and -2.62 kcal/mol (MP2/aug-cc-pVDZ + ZPE + BSSE) were calculated. The two most stable trimers T-A and T-B are very close in energy and have similar infrared spectra. Several weak bands that are in agreement with the calculated frequencies of the trimers T-A and T-B are observed under matrix isolation conditions. However, the differences are too small for a definitive assignment.

Theoretical Study on Effects of Hydrogen-Bonding and Molecule-Cation Interactions on the Sensitivity of HMX.

PubMed

Li, Yunlu; Wu, Junpeng; Cao, Duanlin; Wang, Jianlong

2016-10-04

To assess the effects of weak interactions on the sensitivity of HMX, eleven complexes of HMX (where six of them are hydrogen-bonding complexes, and the other five are molecular-cation complexes) have been studied via quantum chemical treatment. The geometric and electronic structures were determined using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df, 2p) and aug-cc-pVTZ basis sets. The changes of the bond dissociation energy (BDE) of the trigger bond (N-NO2 in HMX) and nitro group charge have been computed on the detail consideration to access the sensitivity changes of HMX. The results indicate that upon complex forming, the BDE increases and the charge of nitro group turns more negative in complexes, suggesting that the strength of the N-NO2 trigger bond is enhanced then the sensitivity of HMX is reduced. Atom-in-molecules analysis have also been carried to understand the nature of intermolecular interactions and the strength of trigger bonds.

3-Amino-1,2,4-triazolium ion in [24(3at)]Cl and [24(3at)]2SnCl6·H2O. Comparative X-ray, vibrational and theoretical studies

NASA Astrophysics Data System (ADS)

Daszkiewicz, Marek; Marchewka, Mariusz K.

2012-09-01

Crystal structures of 3-amino-1,2,4-triazolium chloride and bis(3-amino-1,2,4-triazolium) hexachloridostannate monohydrate were determined by means of X-ray single crystal diffraction. The route of protonation of organic molecule and tautomer equilibrium constants for the cationic forms were calculated using B3LYP/6-31G* method. The most stable protonated species is 2,4-H2-3-amino-1,2,4-triazolium ion, 24(3at)+. Very good agreement between theoretical and experimental frequencies was achieved due to very weak interactions existing in studied compounds. Significantly weaker intermolecular interactions are found in [24(3at)]2SnCl6·H2O than in [24(3at)]Cl. The differences in strength of interactions are manifested in red and blue shifts for stretching and bending motions, respectively. PED calculations show that for 24(3at)+ ion the stretching type of motion of two Nringsbnd H bonds is independent, whereas bending is coupled.

Resolution of 2-chloromandelic acid with (R)-(+)-N-benzyl-1-phenylethylamine: chiral discrimination mechanism.

PubMed

Peng, Yangfeng; He, Quan; Rohani, Sohrab; Jenkins, Hilary

2012-05-01

During the resolution of 2-chloromandelic acid with (R)-(+)-N-benzyl-1-phenylethylamine, the crystals of the less soluble salt were grown, and their structure were determined and presented. The chiral discrimination mechanism was investigated by examining the weak intermolecular interactions (such as hydrogen bond, CH/π, and van der Waals interactions) and molecular packing mode in crystal structure of the less soluble diastereomeric salt. A one-dimensional double-chain hydrogen-bonding network and a "lock-and-key" supramolecular packing mode are disclosed. The investigation demonstrates that hydrophobic layers with corrugated surfaces can fit into the grooves of one another to realize a compact packing, when the molecular structure of resolving agent is much larger than that of the racemate. This "lock-and-key" assembly is recognized to be another characteristic of molecular packing contributing to the chiral discrimination, in addition to the well-known sandwich-like packing by hydrophobic layers with planar boundary surfaces. Copyright © 2012 Wiley Periodicals, Inc.

A general range-separated double-hybrid density-functional theory

NASA Astrophysics Data System (ADS)

Kalai, Cairedine; Toulouse, Julien

2018-04-01

A range-separated double-hybrid (RSDH) scheme which generalizes the usual range-separated hybrids and double hybrids is developed. This scheme consistently uses a two-parameter Coulomb-attenuating-method (CAM)-like decomposition of the electron-electron interaction for both exchange and correlation in order to combine Hartree-Fock exchange and second-order Møller-Plesset (MP2) correlation with a density functional. The RSDH scheme relies on an exact theory which is presented in some detail. Several semi-local approximations are developed for the short-range exchange-correlation density functional involved in this scheme. After finding optimal values for the two parameters of the CAM-like decomposition, the RSDH scheme is shown to have a relatively small basis dependence and to provide atomization energies, reaction barrier heights, and weak intermolecular interactions globally more accurate or comparable to range-separated MP2 or standard MP2. The RSDH scheme represents a new family of double hybrids with minimal empiricism which could be useful for general chemical applications.

Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.

PubMed

Fun, Hoong-Kun; Chantrapromma, Suchada; Salae, Abdul Wahab; Razak, Ibrahim Abdul; Karalai, Chatchanok

2011-05-01

The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ▶). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H⋯O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions. The packing also features C⋯O [3.131 (3) Å] short contacts.

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions

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

Shimada, Rintaro; Hamaguchi, Hiro-o, E-mail: hhama@nctu.edu.tw

2014-05-28

We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of themore » observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of β-carotene with the vibrations of a proximate solvent molecule through solute–solvent dipole–dipole and dipole–quadrupole interactions. It is shown that the infrared active modes arise from the dipole–dipole interaction, whereas Raman active modes from the dipole–quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å.« less

Investigation of intermolecular interactions in finasteride drug crystals in view of X-ray and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Bojarska, Joanna; Maniukiewicz, Waldemar

2015-11-01

The N,N-dimethylformamide (DMF) solvate hemihydrate (1) of finasteride, has been structurally characterized by single-crystal X-ray diffraction at 100 K and compared with previously reported finasteride crystalline forms. In addition, in order to resolve ambiguity concerning H-bond interactions, the crystal structure of finasteride hemihydrate, (2), originally reported by Schultheiss et al. in 2009, has been redetermined with higher precision. The (1) and (2) pseudopolymorphs of finasteride crystallize as orthorhombic in chiral P212121 space group with two very similar host molecules in the asymmetric unit. The conformation of fused 6-membered rings are screw-boat, chair and chair for both molecules, while 5-membered rings assume chair in (1), and half-chair in (2). There is a fairly close resemblance of the molecular geometry for all analyzed compounds, arising due to the rigid host molecule. Inter- and intramolecular host-host, host-guest strong O-H⋯O, N-H⋯O hydrogen bonds and weak C-H⋯O interactions form 3D net conferring stability to the crystal packing. Finasterides can be classified as synthon pseudopolymorphs. Isostructural solvates crystallizing in the orthorhombic space group P212121, with Z‧ = 2, exhibit R22(8) C22(15) network, monoclinic solvate (Z‧ = 1) possess D11(2), while both orthorhombic and monoclinic polymorphs have C(4) motifs, respectively. The structural similarities and subtle differences have been interpreted in view of the 3D Hirshfeld surface analysis and associated 2D fingerprint plots, which enabled detailed qualitative and quantitative insight into the intermolecular interactions. The 97-100% of Hirshfeld surface areas are due to H···H, O···H/H⋯O, C···H/H⋯C and N⋯H/H⋯N contacts. Furthermore, the electrostatic potential has been mapped over the Hirshfeld surfaces to decode the electrostatic complementarities, which exist in the crystal packing.

Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity.

PubMed

Qin, Lingyun; Liu, Huili; Chen, Rong; Zhou, Jingjing; Cheng, Xiyao; Chen, Yao; Huang, Yongqi; Su, Zhengding

2017-11-07

The oncoprotein MdmX (mouse double minute X) is highly homologous to Mdm2 (mouse double minute 2) in terms of their amino acid sequences and three-dimensional conformations, but Mdm2 inhibitors exhibit very weak affinity for MdmX, providing an excellent model for exploring how protein conformation distinguishes and alters inhibitor binding. The intrinsic conformation flexibility of proteins plays pivotal roles in determining and predicting the binding properties and the design of inhibitors. Although the molecular dynamics simulation approach enables us to understand protein-ligand interactions, the mechanism underlying how a flexible binding pocket adapts an inhibitor has been less explored experimentally. In this work, we have investigated how the intrinsic flexible regions of the N-terminal domain of MdmX (N-MdmX) affect the affinity of the Mdm2 inhibitor nutlin-3a using protein engineering. Guided by heteronuclear nuclear Overhauser effect measurements, we identified the flexible regions that affect inhibitor binding affinity around the ligand-binding pocket on N-MdmX. A disulfide engineering mutant, N-MdmX C25-C110/C76-C88 , which incorporated two staples to rigidify the ligand-binding pocket, allowed an affinity for nutlin-3a higher than that of wild-type N-MdmX (K d ∼ 0.48 vs K d ∼ 20.3 μM). Therefore, this mutant provides not only an effective protein model for screening and designing of MdmX inhibitors but also a valuable clue for enhancing the intermolecular interactions of the pharmacophores of a ligand with pronounced flexible regions. In addition, our results revealed an allosteric ligand-binding mechanism of N-MdmX in which the ligand initially interacts with a compact core, followed by augmenting intermolecular interactions with intrinsic flexible regions. This strategy should also be applicable to many other protein targets to accelerate drug discovery.

Application of terahertz spectroscopy and theoretical calculation in dimethylurea isomers investigation

NASA Astrophysics Data System (ADS)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Chen, Tao; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-03-01

The characteristic absorption spectra of two structural isomers of dimethylurea(DMU) in 0.6-1.8 THz region have been measured using terahertz time-domain spectroscopy (THZ-TDS) at room temperature. Significant differences have been found between their terahertz spectra and implied that the THZ-TDS is an effective means of identifying structural isomers. To simulate their spectra, calculations on single molecule and cluster of 1,1-DMU and 1,3-DMU were performed, and we found that the cluster calculations using DFT-D3 method are better to predict the experimental spectra. Using the normal mode as displacements in redundant internal coordinates and the GaussView program, most observed THz vibrational modes are assigned to bending and rocking modes related to the intermolecular hydrogen bonding interactions, and twisting mode of ethyl groups. The different spectral features of two isomers mainly arise from different intermolecular hydrogen bonds resulting from different atom arrangements in molecules and different molecule arrangements in crystals. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular hydrogen bonding interactions in 1,1-DMU and 1,3-DMU crystals are visualized. Therefore, we can confirm that THz-TDS can be used as an effective means for the recognition of structural isomers and detection of intermolecular hydrogen bonding interactions in these crystals.

Observation of aggregation triggered by Resonance Energy Transfer (RET) induced intermolecular pairing force.

PubMed

Pan, Xiaoyong; Wang, Weizhi; Ke, Lin; Zhang, Nan

2017-07-20

In this report, we showed the existence of RET induced intermolecular pairing force by comparing their fluorescence behaviors under room illumination vs standing in dark area for either PFluAnt solution or PFluAnt&PFOBT mixture. Their prominent emission attenuation under room illumination brought out the critical role of photo, i.e. RET induced intermolecular pairing force in induction of polymer aggregation. Constant UV-Vis absorption and fluorescence spectra in terms of both peak shapes and maximum wavelengths implied no chemical decomposition was involved. Recoverable fluorescence intensity, fluorescence lifetime as well as NMR spectra further exclude photo induced decomposition. The controllable on/off state of RET induced intermolecular pairing force was verified by the masking effect of outside PFluAnt solution which function as filter to block the excitation of inside PFluAnt and thus off the RET induced intermolecular pairing force. Theoretical calculation suggest that magnitude of RET induced intermolecular pairing force is on the same scale as that of van der Waals interaction. Although the absolute magnitude of RET induced intermolecular pairing force was not tunable, its effect can be magnified by intentionally turn it "on", which was achieved by irradiance with 5 W desk lamp in this report.

Student Understanding of Intermolecular Forces: A Multimodal Study

ERIC Educational Resources Information Center

Cooper, Melanie M.; Williams, Leah C.; Underwood, Sonia M.

2015-01-01

The ability to use representations of molecular structure to predict the macroscopic properties of a substance is central to the development of a robust understanding of chemistry. Intermolecular forces (IMFs) play an important role in this process because they provide a mechanism for how and why molecules interact. In this study, we investigate…

THE INTERACTION OF PARAMAGNETIC RELAXATION REAGENTS WITH INTRA- AND INTERMOLECULAR HYDROGEN BONDED PHENOLS

EPA Science Inventory

Intermolecular electron-nuclear 13-C relaxation times (T(1)sup e's) from solutions containing the paramagnetic relaxation reagent (PARR), Cr(acac)3, used in conjunction with 13-C T(1)'s in diamagnetic solutions (intramolecular 13-C - (1)H dipolar T(1)'s) provide a significant inc...

Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: probing inter-molecular interactions using PFG NMR.

PubMed

D'Agostino, Carmine; Gladden, Lynn F; Mantle, Mick D; Abbott, Andrew P; Ahmed, Essa I; Al-Murshedi, Azhar Y M; Harris, Robert C

2015-06-21

Pulsed field gradient (PFG) NMR has been used to probe self-diffusion of molecular and ionic species in aqueous mixtures of choline chloride (ChCl) based deep eutectic solvents (DESs), in order to elucidate the effect of water on motion and inter-molecular interactions between the different species in the mixtures, namely the Ch(+) cation and hydrogen bond donor (HBD). The results reveal an interesting and complex behaviour of such mixtures at a molecular level. In general, it is observed that the hydroxyl protons ((1)H) of Ch(+) and the hydrogen bond donor have diffusion coefficients significantly different from those measured for their parent molecules when water is added. This indicates a clear and significant change in inter-molecular interactions. In aqueous Ethaline, the hydroxyl species of Ch(+) and HBD show a stronger interaction with water as water is added to the system. In the case of Glyceline, water has little effect on both hydroxyl proton diffusion of Ch(+) and HBD. In Reline, it is likely that water allows the formation of small amounts of ammonium hydroxide. The most surprising observation is from the self-diffusion of water, which is considerably higher that expected from a homogeneous liquid. This leads to the conclusion that Reline and Glyceline form mixtures that are inhomogeneous at a microscopic level despite the hydrophilicity of the salt and HBD. This work shows that PFG NMR is a powerful tool to elucidate both molecular dynamics and inter-molecular interactions in complex liquid mixtures, such as the aqueous DES mixtures.

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

Torii, Hajime, E-mail: torii.hajime@shizuoka.ac.jp

The intensity of the band at ∼200 cm{sup −1} (∼6 THz) in the Terahertz spectrum of liquid water mainly arises from the modulations of the extent of intermolecular charge transfer through hydrogen bonds, called intermolecular charge fluxes, occurring upon molecular translations along the O…H hydrogen bonds. To obtain reasonable spectral profiles from simulations, it is necessary to effectively incorporate the effects of those intermolecular charge fluxes, but apparently it is not possible by simple classical molecular dynamics simulations with fixed atomic partial charges even if they are amended by molecular induced dipoles due to intermolecular electrostatic interactions. The present paper showsmore » how we can do reasonably correct spectral simulations, without resorting to fully ab initio molecular dynamics.« less

Intermolecular artifacts in probe microscope images of C60 assemblies

NASA Astrophysics Data System (ADS)

Jarvis, Samuel Paul; Rashid, Mohammad Abdur; Sweetman, Adam; Leaf, Jeremy; Taylor, Simon; Moriarty, Philip; Dunn, Janette

2015-12-01

Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. To date, studies have been restricted to planar molecular assemblies with small separations between neighboring molecules. Here we report the observation of intermolecular artifacts over much larger distances in 2D assemblies of C60 molecules, with compelling evidence that in our case the tip apex is terminated by a C60 molecule (rather than the CO termination typically exploited in ultrahigh resolution force microscopy). The complete absence of directional interactions such as hydrogen or halogen bonding, the nonplanar structure of C60, and the fullerene termination of the tip apex in our case highlight that intermolecular artifacts are ubiquitous in dynamic force microscopy.

Intermolecular interactions between σ- and π-holes of bromopentafluorobenzene and pyridine: computational and experimental investigations.

PubMed

Yang, Fang-Ling; Yang, Xing; Wu, Rui-Zhi; Yan, Chao-Xian; Yang, Fan; Ye, Weichun; Zhang, Liang-Wei; Zhou, Pan-Pan

2018-04-25

The characters of σ- and π-holes of bromopentafluorobenzene (C6F5Br) enable it to interact with an electron-rich atom or group like pyridine which possesses an electron lone-pair N atom and a π ring. Theoretical studies of intermolecular interactions between C6F5Br and C5H5N have been carried out at the M06-2X/aug-cc-pVDZ level without and with the counterpoise method, together with single point calculations at M06-2X/TZVP, wB97-XD/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels. The σ- and π-holes of C6F5Br exhibiting positive electrostatic potentials make these sites favorably interact with the N atom and the π ring of C5H5N with negative electrostatic potentials, leading to five different dimers connected by a σ-holen bond, a σ-holeπ bond or a π-holeπ bond. Their geometrical structures, characteristics, nature and spectroscopy behaviors were systematically investigated. EDA analyses reveal that the driving forces in these dimers are different. NCI, QTAIM and NBO analyses confirm the existence of intermolecular interactions formed via σ- and π-holes of C6F5Br and the N atom and the π ring of C5H5N. The experimental IR and Raman spectra gave us important information about the formation of molecular complexes between C6F5Br and C5H5N. We expect that the results could provide valuable insights into the investigation of intermolecular interactions involving σ- and π-holes.

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

Probing intermolecular interactions in a diethylcarbamazine citrate salt by fast MAS 1H solid-state NMR spectroscopy and GIPAW calculations.

PubMed

Venâncio, Tiago; Oliveira, Lyege Magalhaes; Ellena, Javier; Boechat, Nubia; Brown, Steven P

2017-10-01

Fast magic-angle spinning (MAS) NMR is used to probe intermolecular interactions in a diethylcarbamazine salt, that is widely used as a treatment against adult worms of Wuchereria bancrofti which cause a common disease in tropical countries named filariasis. Specifically, a dihydrogen citrate salt that has improved thermal stability and solubility as compared to the free form is studied. One-dimensional 1 H, 13 C and 15 N and two-dimensional 1 H- 13 C and 14 N- 1 H heteronuclear correlation NMR experiments under moderate and fast MAS together with GIPAW (CASTEP) calculations enable the assignment of the 1 H, 13 C and 14 N/ 15 N resonances. A two-dimensional 1 H- 1 H double-quantum (DQ) -single-quantum (SQ) MAS spectrum recorded with BaBa recoupling at 60kHz MAS identifies specific proton-proton proximities associated with citrate-citrate and citrate-diethylcarbamazine intermolecular interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Similarity-transformed perturbation theory on top of truncated local coupled cluster solutions: Theory and applications to intermolecular interactions

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

Azar, Richard Julian, E-mail: julianazar2323@berkeley.edu; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu

2015-05-28

Your correspondents develop and apply fully nonorthogonal, local-reference perturbation theories describing non-covalent interactions. Our formulations are based on a Löwdin partitioning of the similarity-transformed Hamiltonian into a zeroth-order intramonomer piece (taking local CCSD solutions as its zeroth-order eigenfunction) plus a first-order piece coupling the fragments. If considerations are limited to a single molecule, the proposed intermolecular similarity-transformed perturbation theory represents a frozen-orbital variant of the “(2)”-type theories shown to be competitive with CCSD(T) and of similar cost if all terms are retained. Different restrictions on the zeroth- and first-order amplitudes are explored in the context of large-computation tractability and elucidationmore » of non-local effects in the space of singles and doubles. To accurately approximate CCSD intermolecular interaction energies, a quadratically growing number of variables must be included at zeroth-order.« less

Structure and Electronic Properties of Nano-complex CCl4…Cr(AcacCl)3 on Evidence Derived from Vibrational Spectroscopy

NASA Astrophysics Data System (ADS)

Slabzhennikov, S. N.; Kuarton, L. A.; Ryabchenko, O. B.

In order to specify influence of intermolecular interaction on IR spectrum of interacting species, an investigation of a process CCl4 + Cr(AcacCl)3 → CCl4…Cr(AcacCl)3 has been performed by means of Hartree-Fock-Roothaan method in MIDI basis set with p- and d- polarization functions. An estimation of intermolecular interaction in geometrical parameters, electron density function both between interacting particles and inside themselves, frequencies and intensities of normal modes has been carried out. Chemical bonds with the most significant shifts of characteristics under formation of nano-complex CCl4…Cr(AcacCl)3 have been noted.

Students' Understanding of Boiling Points and Intermolecular Forces

ERIC Educational Resources Information Center

Schmidt, Hans-Jurgen; Kaufmann, Birgit; Treagust, David F.

2009-01-01

In introductory chemistry courses students are presented with the model that matter is composed of particles, and that weak forces of attraction exist between them. This model is used to interpret phenomena such as solubility and melting points, and aids in understanding the changes in states of matter as opposed to chemical reactions. We…

Organic molecules on metal and oxide semiconductor substrates: Adsorption behavior and electronic energy level alignment

NASA Astrophysics Data System (ADS)

Ruggieri, Charles M.

Modern devices such as organic light emitting diodes use organic/oxide and organic/metal interfaces for crucial processes such as charge injection and charge transfer. Understanding fundamental physical processes occurring at these interfaces is essential to improving device performance. The ultimate goal of studying such interfaces is to form a predictive model of interfacial interactions, which has not yet been established. To this end, this thesis focuses on obtaining a better understanding of fundamental physical interactions governing molecular self-assembly and electronic energy level alignment at organic/metal and organic/oxide interfaces. This is accomplished by investigating both the molecular adsorption geometry using scanning tunneling microscopy, as well as the electronic structure at the interface using direct and inverse photoemission spectroscopy, and analyzing the results in the context of first principles electronic structure calculations. First, we study the adsorption geometry of zinc tetraphenylporphyrin (ZnTPP) molecules on three noble metal surfaces: Au(111), Ag(111), and Ag(100). These surfaces were chosen to systematically compare the molecular self-assembly and adsorption behavior on two metals of the same surface symmetry and two surface symmetries of one metal. From this investigation, we improve the understanding of self-assembly at organic/metal interfaces and the relative strengths of competing intermolecular and molecule-substrate interactions that influence molecular adsorption geometry. We then investigate the electronic structure of the ZnTPP/Au(111), Ag(111), and Ag(100) interfaces as examples of weakly-interacting systems. We compare these cases to ZnTPP on TiO2(110), a wide-bandgap oxide semiconductor, and explain the intermolecular and molecule-substrate interactions that determine the electronic energy level alignment at the interface. Finally we study tetracyanoquinodimethane (TCNQ), a strong electron acceptor, on TiO2(110), which exhibits chemical hybridization accompanied by molecular distortion, as well as extreme charge transfer resulting in the development of a space charge layer in the oxide. Thus, we present a broad experimental and theoretical perspective on the study of organic/metal and organic/oxide interfaces, elucidating fundamental physical interactions that govern molecular organization and energy level alignment.

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

PubMed

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

2012-09-01

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

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

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

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Role of Polymorphism and Thin-Film Morphology in Organic Semiconductors Processed by Solution Shearing

PubMed Central

2018-01-01

Organic semiconductors (OSCs) are promising materials for cost-effective production of electronic devices because they can be processed from solution employing high-throughput techniques. However, small-molecule OSCs are prone to structural modifications because of the presence of weak van der Waals intermolecular interactions. Hence, controlling the crystallization in these materials is pivotal to achieve high device reproducibility. In this perspective article, we focus on controlling polymorphism and morphology in small-molecule organic semiconducting thin films deposited by solution-shearing techniques compatible with roll-to-roll systems. Special attention is paid to the influence that the different experimental deposition parameters can have on thin films. Further, the main characterization techniques for thin-film structures are reviewed, highlighting the in situ characterization tools that can provide crucial insights into the crystallization mechanisms. PMID:29503976

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE PAGES

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

2017-05-15

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

2-Hy-droxy-16-[(E)-4-methyl-benzyl-idene]-13-(4-methyl-phen-yl)-12-phenyl-1,11-diaza-penta-cyclo-[12.3.1.0.0.0]octa-deca-3(8),4,6-triene-9,15-dione.

PubMed

Kumar, Raju Suresh; Osman, Hasnah; Abdul Rahim, Aisyah Saad; Goh, Jia Hao; Fun, Hoong-Kun

2010-07-24

In the title compound, C(37)H(32)N(2)O(3), an intra-molecular O-H⋯N hydrogen bond generates a five-membered ring, producing an S(5) motif. The piperidone ring adopts a half-chair conformation. The two fused pyrrolidine rings have similar envelope conformations. The interplanar angles between the benzene rings A/B and C/D are 75.68 (7) and 30.22 (6)°, respectively. In the crystal structure, adjacent mol-ecules are inter-connected into chains propagating along the [010] direction via inter-molecular C-H⋯O hydrogen bonds. Further stabilization is provided by weak C-H⋯π inter-actions.

Crystallization of amorphous solid dispersions of resveratrol during preparation and storage-Impact of different polymers.

PubMed

Wegiel, Lindsay A; Mauer, Lisa J; Edgar, Kevin J; Taylor, Lynne S

2013-01-01

The objective of this study was to investigate intermolecular interactions between resveratrol and polymers in amorphous blends and to study the potential correlations between compound-polymer interactions, manufacturability, and stability of the amorphous system to crystallization during storage. Polymers included two grades of poly (vinylpyrrolidone) (PVP), Eudragit E100 (E100), hydroxypropyl methylcellulose (HPMC), hydroxypropyl methylcellulose acetate succinate (HPMCAS), carboxymethyl cellulose acetate butyrate, and poly (acrylic acid) (PAA). Amorphous blends ("solid dispersions") were prepared by dissolving both resveratrol and polymer in a solvent followed by rotary evaporation. Crystallinity was evaluated using X-ray powder diffraction and was studied as a function of time. Mid-infrared (IR) spectroscopy was used to investigate resveratrol-polymer interactions. Polymer influence on the crystallization behavior of resveratrol varied and could be correlated to the polymer structure, whereby polymers with good hydrogen bond acceptor groups performed better as crystallization inhibitors. Resveratrol-polymer hydrogen bonding interactions could be inferred from the IR spectra. Somewhat surprisingly, E100 and resveratrol showed evidence of an acid-base reaction, in addition to intermolecular hydrogen bonding interactions. PVP K29/32 appeared to form stronger hydrogen bond interactions with resveratrol relative to HPMC, HPMCAS, and PAA, consistent with acceptor group chemistry. Long-term stability of the systems against crystallization suggested that stability is linked to the type and strength of intermolecular interactions present. whereby resveratrol blended with E100 and PVP K29/32 showed the greatest stability to crystallization. In conclusion, amorphous resveratrol is unstable and difficult to form, requiring the assistance of a polymeric crystallization inhibitor to facilitate the formation of an amorphous solid dispersion. Polymers effective at inhibiting crystallization were identified, and it is rationalized that their effectiveness is based on the type and strength of their intermolecular interactions with resveratrol. Copyright © 2012 Wiley Periodicals, Inc.

Role of Intramolecular Aromatic π-π Interactions in the Self-Assembly of Di-l-Phenylalanine Dipeptide Driven by Intermolecular Interactions: Effect of Alanine Substitution.

PubMed

Reddy, Samala Murali Mohan; Shanmugam, Ganesh

2016-09-19

Although the role of intermolecular aromatic π-π interactions in the self-assembly of di-l-phenylalanine (l-Phe-l-Phe, FF), a peptide that is known for hierarchical structure, is well established, the influence of intramolecular π-π interactions on the morphology of the self-assembled structure of FF has not been studied. Herein, the role of intramolecular aromatic π-π interactions is investigated for FF and analogous alanine (Ala)-containing dipeptides, namely, l-Phe-l-Ala (FA) and l-Ala-l-Phe (AF). The results reveal that these dipeptides not only form self-assemblies, but also exhibit remarkable differences in structural morphology. The morphological differences between FF and the analogues indicate the importance of intramolecular π-π interactions, and the structural difference between FA and AF demonstrates the crucial role of the nature of intramolecular side-chain interactions (aromatic-aliphatic or aliphatic-aromatic), in addition to intermolecular interactions, in deciding the final morphology of the self-assembled structure. The current results emphasise that intramolecular aromatic π-π interaction may not be essential to induce self-assembly in smaller peptides, and π (aromatic)-alkyl or alkyl-π (aromatic) interactions may be sufficient. This work also illustrates the versatility of aromatic and a combination of aromatic and aliphatic residues in dipeptides in the formation of structurally diverse self-assembled structures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

(Carbonyl-1κC)bis-[2,3(η)-cyclo-penta-dien-yl][μ(3)-(S-methyl trithio-carbonato)methylidyne-1:2:3κC,S'':C:C](triphenyl-phosphine-1κP)(μ(3)-sulfido-1:2:3κS)dicobalt(II)iron(II) trifluoro-methane-sulfonate.

PubMed

Manning, Anthony R; McAdam, C John; Palmer, Anthony J; Simpson, Jim

2008-04-10

The asymmetric unit of the title compound, [FeCo(2)(C(5)H(5))(2)(C(3)H(3)S(3))S(C(18)H(15)P)(CO)]CF(3)SO(3), consists of a triangular irondicobalt cluster cation and a trifluoro-methane-sulfonate anion. In the cation, the FeCo(2) triangle is symmetrically capped on one face by an S atom and on the other by a C atom linked to a methyl trithio-carbonate residue that bridges the Fe-C bond. Each Co atom carries a cyclo-penta-dienyl ligand while the Fe atom coordinates to one carbonyl and one triphenyl-phosphine ligand. In the crystal structure, the cation is linked to the anion by a number of weak non-classical C-H⋯O and C-H⋯F hydrogen bonds and weak S⋯O (3.317 Å) and S⋯F (3.198 Å) inter-actions. The structure is further stabilized by additional inter-molecular C-H⋯O, C-H⋯F and O⋯O (2.942 Å) contacts, together with an unusual S⋯π(Cp) inter-action (S⋯centroid distance = 3.385 Å), generating an extended network.

Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

PubMed

Frembgen-Kesner, Tamara; Elcock, Adrian H

2010-11-03

Theory and computation have long been used to rationalize the experimental association rate constants of protein-protein complexes, and Brownian dynamics (BD) simulations, in particular, have been successful in reproducing the relative rate constants of wild-type and mutant protein pairs. Missing from previous BD studies of association kinetics, however, has been the description of hydrodynamic interactions (HIs) between, and within, the diffusing proteins. Here we address this issue by rigorously including HIs in BD simulations of the barnase-barstar association reaction. We first show that even very simplified representations of the proteins--involving approximately one pseudoatom for every three residues in the protein--can provide excellent reproduction of the absolute association rate constants of wild-type and mutant protein pairs. We then show that simulations that include intermolecular HIs also produce excellent estimates of association rate constants, but, for a given reaction criterion, yield values that are decreased by ∼35-80% relative to those obtained in the absence of intermolecular HIs. The neglect of intermolecular HIs in previous BD simulation studies, therefore, is likely to have contributed to the somewhat overestimated absolute rate constants previously obtained. Consequently, intermolecular HIs could be an important component to include in accurate modeling of the kinetics of macromolecular association events. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations.

PubMed

Zgarbová, Marie; Otyepka, Michal; Sponer, Jirí; Hobza, Pavel; Jurecka, Petr

2010-09-21

The intermolecular interaction energy components for several molecular complexes were calculated using force fields available in the AMBER suite of programs and compared with Density Functional Theory-Symmetry Adapted Perturbation Theory (DFT-SAPT) values. The extent to which such comparison is meaningful is discussed. The comparability is shown to depend strongly on the intermolecular distance, which means that comparisons made at one distance only are of limited value. At large distances the coulombic and van der Waals 1/r(6) empirical terms correspond fairly well with the DFT-SAPT electrostatics and dispersion terms, respectively. At the onset of electronic overlap the empirical values deviate from the reference values considerably. However, the errors in the force fields tend to cancel out in a systematic manner at equilibrium distances. Thus, the overall performance of the force fields displays errors an order of magnitude smaller than those of the individual interaction energy components. The repulsive 1/r(12) component of the van der Waals expression seems to be responsible for a significant part of the deviation of the force field results from the reference values. We suggest that further improvement of the force fields for intermolecular interactions would require replacement of the nonphysical 1/r(12) term by an exponential function. Dispersion anisotropy and its effects are discussed. Our analysis is intended to show that although comparing the empirical and non-empirical interaction energy components is in general problematic, it might bring insights useful for the construction of new force fields. Our results are relevant to often performed force-field-based interaction energy decompositions.

2'-Chloro-4-meth-oxy-3-nitro-benzil.

PubMed

Nithya, G; Thanuja, B; Chakkaravarthi, G; Kanagam, Charles C

2011-06-01

In the title compound, C(15)H(10)ClNO(5), the dihedral angle between the aromatic rings is 87.99 (5)°. The O-C-C-O torsion angle between the two carbonyl units is -119.03 (16)°. The crystal structure is stabilized by a weak intermolecular C-H⋯O hydrogen bond.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Pressure induced enhancement of the magnetic ordering temperature in rhenium(IV) monomers

NASA Astrophysics Data System (ADS)

Woodall, Christopher H.; Craig, Gavin A.; Prescimone, Alessandro; Misek, Martin; Cano, Joan; Faus, Juan; Probert, Michael R.; Parsons, Simon; Moggach, Stephen; Martínez-Lillo, José; Murrie, Mark; Kamenev, Konstantin V.; Brechin, Euan K.

2016-12-01

Materials that demonstrate long-range magnetic order are synonymous with information storage and the electronics industry, with the phenomenon commonly associated with metals, metal alloys or metal oxides and sulfides. A lesser known family of magnetically ordered complexes are the monometallic compounds of highly anisotropic d-block transition metals; the `transformation' from isolated zero-dimensional molecule to ordered, spin-canted, three-dimensional lattice being the result of through-space interactions arising from the combination of large magnetic anisotropy and spin-delocalization from metal to ligand which induces important intermolecular contacts. Here we report the effect of pressure on two such mononuclear rhenium(IV) compounds that exhibit long-range magnetic order under ambient conditions via a spin canting mechanism, with Tc controlled by the strength of the intermolecular interactions. As these are determined by intermolecular distance, `squeezing' the molecules closer together generates remarkable enhancements in ordering temperatures, with a linear dependence of Tc with pressure.

Synthesis and structural characterization of some trisulfide analoges of thiouracil-based antithyroid drugs

NASA Astrophysics Data System (ADS)

Bhabak, Krishna P.; Bhowmick, Debasish

2012-08-01

Thiourea-based antithyroid drugs are effectively used for the treatment of hyperthyroidism. In this paper, we describe the synthesis of new trisulfides (11-12) from the commonly used thiourea-based antithyroid drugs such as 6-n-propyl-2-thiouracil (PTU) and 6-methyl-2-thiouracil (MTU) in the reaction with I2/KI system. Structural analysis by single crystal X-ray diffraction studies revealed the stabilization of trisulfides by a lactam-lactim tautomerism facilitating effective intramolecular as well as intermolecular non-covalent interactions. Although the structures of both trisulfides were found to be quite similar, a notable difference in the intermolecular interactions was observed between compounds 11 and 12 leading to different structural patterns. Structural stabilization of these trisulfides by tautomerism followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule.

Exploring the Details of Intermolecular Interactions via a Systematic Characterization of the Structures of the Bimolecular Heterodimers Formed Between Protic Acids and Haloethylenes

NASA Astrophysics Data System (ADS)

Leung, Helen O.

2017-06-01

In the early 2000's, the work of Cole and Legon, combined with that done earlier by Kisiel, Fowler, and Legon, demonstrated that comparisons among the complexes of HF, HCl, and HCCH each with vinyl fluoride could provide information concerning the strength of intermolecular interactions. Specifically, that the length of the hydrogen bond and its deviation from linearity as a result of a secondary interaction with the nucleophilic portion of the protic acid could be correlated with the hydrogen bond strength. Building on this foundation, we undertook a systematic characterization of the molecular structures of complexes formed between these three acids and the remaining polar fluoroethylenes, seeking to unravel the nature of their intermolecular interactions. What started out as a simple confirmation of chemical intuition regarding relative interaction strengths developed into a fuller appreciation of the competition between electrostatic and steric forces in determining the lowest energy configuration for the heterodimer. Additional surprises were in store for us as we expanded the study to chlorofluoroethylenes. Although the first few examples again served to confirm earlier conclusions, subsequent complexes provided unexpected results that signaled an increasing importance of the dispersion interaction in determining the geometry of the complex as well as the fundamental differences in the electron distributions surrounding the halogens in a C-F versus C-Cl bond. Our work with these species has not only allowed us to investigate fundamental questions regarding intermolecular interactions, but obtaining and analyzing the spectra of these complexes along with those of the various haloethylene monomers and their complexes with the argon atom have provided an introduction to molecular spectroscopy and structure determination for many undergraduate students. G.C. Cole and A.C. Legon, Chem. Phys. Lett. 369, 31-40 (2003). G.C. Cole and A.C. Legon, Chem. Phys. Lett. 400, 414-424 (2004). Z. Kisiel, P.W. Fowler, and A.C. Legon, J. Chem. Phys. 93, 3054-3062 (1990).

Development and Implementation of a Protein-Protein Binding Experiment to Teach Intermolecular Interactions in High School or Undergraduate Classrooms

ERIC Educational Resources Information Center

Johnson, Sadie M.; Javner, Cassidy; Hackel, Benjamin J.

2017-01-01

The goal of this study was to create an accessible, inexpensive, and engaging experiment to teach high school and undergraduate chemistry or biology students about intermolecular forces and how they contribute to the behavior of biomolecules. We developed an enzyme-linked immunosorbent assay (ELISA) to probe specific structure-function…

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

PubMed Central

Nagy, Peter I.

2014-01-01

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions.

PubMed Central

Keskin, O.; Bahar, I.; Badretdinov, A. Y.; Ptitsyn, O. B.; Jernigan, R. L.

1998-01-01

Whether knowledge-based intra-molecular inter-residue potentials are valid to represent inter-molecular interactions taking place at protein-protein interfaces has been questioned in several studies. Differences in the chain connectivity effect and in residue packing geometry between interfaces and single chain monomers have been pointed out as possible sources of distinct energetics for the two cases. In the present study, the interfacial regions of protein-protein complexes are examined to extract inter-molecular inter-residue potentials, using the same statistical methods as those previously adopted for intra-molecular residue pairs. Two sets of energy parameters are derived, corresponding to solvent-mediation and "average residue" mediation. The former set is shown to be highly correlated (correlation coefficient 0.89) with that previously obtained for inter-residue interactions within single chain monomers, while the latter exhibits a weaker correlation (0.69) with its intra-molecular counterpart. In addition to the close similarity of intra- and inter-molecular solvent-mediated potentials, they are shown to be significantly more residue-specific and thereby discriminative compared to the residue-mediated ones, indicating that solvent-mediation plays a major role in controlling the effective inter-residue interactions, either at interfaces, or within single monomers. Based on this observation, a reduced set of energy parameters comprising 20 one-body and 3 two-body terms is proposed (as opposed to the 20 x 20 tables of inter-residue potentials), which reproduces the conventional 20 x 20 tables with a correlation coefficient of 0.99. PMID:9865952

Modeling Adsorption-Desorption Processes at the Intermolecular Interactions Level

NASA Astrophysics Data System (ADS)

Varfolomeeva, Vera V.; Terentev, Alexey V.

2018-01-01

Modeling of the surface adsorption and desorption processes, as well as the diffusion, are of considerable interest for the physical phenomenon under study in ground tests conditions. When imitating physical processes and phenomena, it is important to choose the correct parameters to describe the adsorption of gases and the formation of films on the structural materials surface. In the present research the adsorption-desorption processes on the gas-solid interface are modeled with allowance for diffusion. Approaches are proposed to describe the adsorbate distribution on the solid body surface at the intermolecular interactions level. The potentials of the intermolecular interaction of water-water, water-methane and methane-methane were used to adequately modeling the real physical and chemical processes. The energies calculated by the B3LYP/aug-cc-pVDZ method. Computational algorithms for determining the average molecule area in a dense monolayer, are considered here. Differences in modeling approaches are also given: that of the proposed in this work and the previously approved probabilistic cellular automaton (PCA) method. It has been shown that the main difference is due to certain limitations of the PCA method. The importance of accounting the intermolecular interactions via hydrogen bonding has been indicated. Further development of the adsorption-desorption processes modeling will allow to find the conditions for of surface processes regulation by means of quantity adsorbed molecules control. The proposed approach to representing the molecular system significantly shortens the calculation time in comparison with the use of atom-atom potentials. In the future, this will allow to modeling the multilayer adsorption at a reasonable computational cost.

3-Methylthio-4-phenyl-5-phenylamino-1,2,4-triazole hexabromotellurate:X-ray and computational study

NASA Astrophysics Data System (ADS)

Fizer, Maksym; Slivka, Mikhailo; Mariychuk, Ruslan; Baumer, Vjacheslav; Lendel, Vasil

2018-06-01

The structure of a newly synthesized 3-methylthio-4-phenyl-5-phenylamino-1,2,4-triazole 1 and its hexabromotellurate salt 2 was investigated. The X-ray diffraction study of 2 gives the insight on the different interaction types in the crystal. The DFT calculations were used for the comprehensive study of the intramolecular and intermolecular forces that are present in the title 3-methylthio-4-phenyl-5-phenylamino-1,2,4-triazole hexabromotellurate. The presence of three different aromatic moieties in the investigated compounds cause π-π stacking interactions which were studied through the Hirshfeld surface analysis and with the discrimination of weak interaction types by filling color to a reduced density gradient (RDG) function isosurface. The RDG in the crystalline state was calculated upon experimental molecular geometry by partitions of the crystal to QM part that was calculated at M06-L/6-311G(d,p) level, and the semi-empirical QM part that was modeled with the PM7 method in QM/MM-like manner. The reactivity of 3-methylthio-4-phenyl-5-phenylamino-1,2,4-triazole and its protonated form was also discussed in terms of conceptual DFT theory and it shows the tendency of sulfur to be the most active center in an electrophilic and radical attack, whereas the site for nucleophilic substitution is medium dependent and not an unequivocal. NICS(1) index was used for the analysis of aromaticity of three different cyclic moieties. The present study insights the changes in the structure of a polyfunctional substituted triazole upon its protonation and explains these changes with the analysis of weak interactions.

Spin relaxation measurements of electrostatic bias in intermolecular exploration

NASA Astrophysics Data System (ADS)

Teng, Ching-Ling; Bryant, Robert G.

2006-04-01

We utilize the paramagnetic contribution to proton spin-lattice relaxation rate constants induced by freely diffusing charged paramagnetic centers to investigate the effect of charge on the intermolecular exploration of a protein by the small molecule. The proton NMR spectrum provided 255 resolved resonances that report how the explorer molecule local concentration varies with position on the surface. The measurements integrate over local dielectric constant variations, and, in principle, provide an experimental characterization of the surface free energy sampling biases introduced by the charge distribution on the protein. The experimental results for ribonuclease A obtained using positive, neutral, and negatively charged small nitroxide radicals are qualitatively similar to those expected from electrostatic calculations. However, while systematic electrostatic trends are apparent, the three different combinations of the data sets do not yield internally consistent values for the electrostatic contribution to the intermolecular free energy. We attribute this failure to the weakness of the electrostatic sampling bias for charged nitroxides in water and local variations in effective translational diffusion constant at the water-protein interface, which enters the nuclear spin relaxation equations for the nitroxide-proton dipolar coupling.

Thermodynamic curvature for attractive and repulsive intermolecular forces

NASA Astrophysics Data System (ADS)

May, Helge-Otmar; Mausbach, Peter; Ruppeiner, George

2013-09-01

The thermodynamic curvature scalar R for the Lennard-Jones system is evaluated in phase space, including vapor, liquid, and solid state. We paid special attention to the investigation of R along vapor-liquid, liquid-solid, and vapor-solid equilibria. Because R is a measure of interaction strength, we traced out the line R=0 dividing the phase space into regions with effectively attractive (R<0) or repulsive (R>0) interactions. Furthermore, we analyzed the dependence of R on the strength of attraction applying a perturbation ansatz proposed by Weeks-Chandler-Anderson. Our results show clearly a transition from R>0 (for poorly repulsive interaction) to R<0 when loading attraction in the intermolecular potential.

Structure and bonding in beta-HMX-characterization of a trans-annular N...N interaction.

PubMed

Zhurova, Elizabeth A; Zhurov, Vladimir V; Pinkerton, A Alan

2007-11-14

Chemical bonding in the beta-phase of the 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) crystal based on the experimental electron density obtained from X-ray diffraction data at 20 K, and solid state theoretical calculations, has been analyzed in terms of the quantum theory of atoms in molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. An unusual N...N bonding interaction across the 8-membered ring has been discovered and characterized. Hydrogen bonding, O...O and O...C intermolecular interactions are reported. Atomic charges and features of the electrostatic potential are discussed.

The structural basis for the negative regulation of thioredoxin by thioredoxin-interacting protein

PubMed Central

Hwang, Jungwon; Suh, Hyun-Woo; Jeon, Young Ho; Hwang, Eunha; Nguyen, Loi T.; Yeom, Jeonghun; Lee, Seung-Goo; Lee, Cheolju; Kim, Kyung Jin; Kang, Beom Sik; Jeong, Jin-Ok; Oh, Tae-Kwang; Choi, Inpyo; Lee, Jie-Oh; Kim, Myung Hee

2014-01-01

The redox-dependent inhibition of thioredoxin (TRX) by thioredoxin-interacting protein (TXNIP) plays a pivotal role in various cancers and metabolic syndromes. However, the molecular mechanism of this regulation is largely unknown. Here, we present the crystal structure of the TRX–TXNIP complex and demonstrate that the inhibition of TRX by TXNIP is mediated by an intermolecular disulphide interaction resulting from a novel disulphide bond-switching mechanism. Upon binding to TRX, TXNIP undergoes a structural rearrangement that involves switching of a head-to-tail interprotomer Cys63-Cys247 disulphide between TXNIP molecules to an interdomain Cys63-Cys190 disulphide, and the formation of a de novo intermolecular TXNIP Cys247-TRX Cys32 disulphide. This disulphide-switching event unexpectedly results in a domain arrangement of TXNIP that is entirely different from those of other arrestin family proteins. We further show that the intermolecular disulphide bond between TRX and TXNIP dissociates in the presence of high concentrations of reactive oxygen species. This study provides insight into TRX and TXNIP-dependent cellular regulation. PMID:24389582

Thermodynamic balance of perylene self-assembly on Ag(110)

NASA Astrophysics Data System (ADS)

Bobrov, Kirill; Kalashnyk, Nataliya; Guillemot, Laurent

2016-10-01

We present a room temperature STM study of perylene adsorption on Ag(110) at the monolayer coverage regime. We found that structure and symmetry of the perylene monolayer are settled by thermodynamic balance of the three factors: (i) the ability of perylene molecules to recognize specific adsorption sites on the (110) lattice, (ii) the intermolecular interaction, and (iii) the accommodation of thermal motion of the molecules. The moderate strength of the site recognition and the intermolecular interaction, of the same order of magnitude as kT ˜ 25 meV, represents a key feature of the thermodynamic balance. It bestows to this system the unique quality to form the quasi-liquid monolayer of epitaxial as well as self-assembling character. The perylene monolayer accommodates the short-range motion of the molecules instead of quenching it. It precludes the formation of possible solid nuclei and maintains common registry of the included molecules. The surface registry of the quasi-liquid phase is provided by locking of a structure-related fraction of the perylene molecules into specific adsorption sites of the (110) lattice favorable in terms of intermolecular interaction.

Seven organic salts assembled from hydrogen-bonds of N-H⋯O, O-H⋯O, and C-H⋯O between acidic compounds and bis(benzimidazole)

NASA Astrophysics Data System (ADS)

Jin, Shouwen; Liu, Hui; Gao, Xin Jun; Lin, Zhanghui; Chen, Guqing; Wang, Daqi

2014-10-01

Seven crystalline organic acid-base adducts derived from 1,4-bis(benzimidazol-2-yl)butane/1,2-bis(2-benzimidazolyl)-1,2-ethanediol and acidic components (picric acid, 2-hydroxy-5-(phenyldiazenyl)benzoic acid, 5-sulfosalicylic acid, oxalic acid, and 1,5-naphthalenedisulfonic acid) were prepared and characterized by the single crystal X-ray diffraction analysis, IR, mp, and elemental analysis. All of the seven compounds are organic salts involving proton transfer from the acidic components to the bis(benzimidazole). For the salt 3, although a competing carboxyl group is present, it has been observed that only the proton at the -SO3H group is deprotonized rather than the H at the COOH. While in the salt 7, both COOH and SO3H were ionized to exhibit a valence number of -2. For 4, the oxalic acid existed as unionized molecule, monoanion, and dianion simultaneously in one compound. All supramolecular architectures of the organic salts 1-7 involve extensive intermolecular N-H⋯O, O-H⋯O, and C-H⋯O hydrogen bonds as well as other noncovalent interactions. Since the potentially hydrogen bonding phenol group is present in the ortho position to the carboxyl group in 2, 3, and 7, it forms the more facile intramolecular O-H⋯O hydrogen bonding. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, all the complexes displayed 3D framework structure.

Synthesis and characterization of amorphous mesoporous silica using TEMPO-functionalized amphiphilic templates

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

Vries, Wilke de; Doerenkamp, Carsten; Zeng, Zhaoyang

Inorganic–organic hybrid materials based on amorphous mesoporous silica containing organized nitroxide radicals within its mesopores have been prepared using the micellar self-assembly of TEOS solutions containing the nitroxide functionalized amphiphile (4-(N,N-dimethyl-N-hexadecylammonium)-2,2,6, 6-tetramethyl-piperidin-N-oxyl-iodide) (CAT-16). This template has been used both in its pure form and in various mixtures with cetyl trimethylammonium bromide (CTAB). The samples have been characterized by chemical analysis, N{sub 2} sorption studies, magnetic susceptibility measurements, and various spectroscopic methods. While electron paramagnetic resonance (EPR) spectra indicate that the strength of the intermolecular spin–spin interactions can be controlled via the CAT-16/CTAB ratio, nuclear magnetic resonance (NMR) data suggest thatmore » these interactions are too weak to facilitate cooperative magnetism. - Graphical abstract: The amphiphilic radical CAT-16 is used as a template for the synthesis of amorphous mesoporous silica. The resulting paramagnetic hybrid materials are characterized by BET, FTIR, NMR, EPR and magnetic susceptibility studies. - Highlights: • Amphiphilic CAT-16 as a template for mesoporous silica. • Comprehensive structural characterization by BET, FTIR; EPR and NMR. • Strength of radical-radical interactions tuable within CAT-16/CTAB mixtures.« less

Application of London-type dispersion corrections to the solid-state density functional theory simulation of the terahertz spectra of crystalline pharmaceuticals.

PubMed

King, Matthew D; Buchanan, William D; Korter, Timothy M

2011-03-14

The effects of applying an empirical dispersion correction to solid-state density functional theory methods were evaluated in the simulation of the crystal structure and low-frequency (10 to 90 cm(-1)) terahertz spectrum of the non-steroidal anti-inflammatory drug, naproxen. The naproxen molecular crystal is bound largely by weak London force interactions, as well as by more prominent interactions such as hydrogen bonding, and thus serves as a good model for the assessment of the pair-wise dispersion correction term in systems influenced by intermolecular interactions of various strengths. Modifications to the dispersion parameters were tested in both fully optimized unit cell dimensions and those determined by X-ray crystallography, with subsequent simulations of the THz spectrum being performed. Use of the unmodified PBE density functional leads to an unrealistic expansion of the unit cell volume and the poor representation of the THz spectrum. Inclusion of a modified dispersion correction enabled a high-quality simulation of the THz spectrum and crystal structure of naproxen to be achieved without the need for artificially constraining the unit cell dimensions.

Teaching Ion-Ion, Ion-Dipole, and Dipole-Dipole Interactions

ERIC Educational Resources Information Center

Yoder, Claude H.

1977-01-01

Discusses how electrostatic interactions can be taught quantitatively through Coulomb's Law at a variety of points in a chemistry curriculum. Each type of interaction is shown at both the intramolecular and the inter-"molecular" levels. (MR)

Dielectric and spectroscopic study of binary mixture of Acrylonitrile with Chlorobenzene

NASA Astrophysics Data System (ADS)

Deshmukh, Snehal D.; Pattebahadur, K. L.; Mohod, A. G.; Undre, P. B.; Patil, S. S.; Khirade, P. W.

2018-05-01

In this paper, study of binary mixture of Acrylonitrile (ACN) with Chlorobenzene (CBZ) has been carried out at eleven concentrations at room temperature. The determined Dielectric Constant (ɛ0) Density (ρ) and Refractive index (nD) values of binary mixture are used to calculate the excess properties of mixture over the entire composition range and fitted to the Redlich-Kister equation. From the above parameters, intermolecular interaction and dynamics of molecules of binary mixture at molecular level are discussed. The Conformational analysis of the intermolecular interaction between Acrylonitrile and Chlorobenzene is supported by the FTIR spectra.

Thermal and volumetric properties of methanol-hexamethylphosphortriamide mixtures under standard conditions

NASA Astrophysics Data System (ADS)

Batov, D. V.; Kustov, A. V.; Antonova, O. A.; Smirnova, N. L.

2017-02-01

Enthalpic and volumetric characteristics of mixing in a methanol (MeOH)-hexamethylphosphortriamide (HMPT, 2) mixture are studied. Based on an analysis of concentration changes in the obtained data and the calculated partial molar characteristics, it is shown that at 0.2 molar fractions > x 2 > 0.7 molar fractions, the variation in the composition of the mixture slightly alters the character of intermolecular interactions characteristic of pure components. It is found that MeOH-HMPT mixtures experience most changes in intermolecular interaction and structure within the range of 0.2-0.7 molar fractions of HMPT.

The impact of solvent relative permittivity on the dimerisation of organic molecules well below their solubility limits: examples from brewed coffee and beyond.

PubMed

Bradley, Ellen S; Hendon, Christopher H

2017-03-22

The formation of aqueous intermolecular dimers is governed by both the nature and strength of the intermolecular interactions and the entropy of dissolution. The former interaction energies are determined by the polarity of the solvent and the functionality of the solute. Using quantum chemical methods, we probe the energetics of dimer formation of representative compounds found in coffee well below their solubility limits. We find that with the exclusion of entropy, the dimer formation is thermodynamically unfavorable with negligible dependence on the dielectric medium.

The influence of the nature of a substituent on the parameters of the intra- and intermolecular interactions in molecules of cross-conjugated ketones

NASA Astrophysics Data System (ADS)

Kompaneets, V. V.; Vasilieva, I. A.

2017-08-01

We have quantitatively analyzed the vibronic parameters of two cross-conjugated δ-dimethylaminoketones. The presence of the -N(CH3)2, C=O, and -NO2 groups in the benzene ring has been shown to affect the manifestation of the vibronic parameters of characteristic bands that describe the state (vibrations, types of deformation upon excitation) of polyene systems with aromatic rings. Data on the influence of the nature of the substituent on the parameters of intra- and intermolecular interactions in the examined compounds have been presented.

Advanced understanding on electronic structure of molecular semiconductors and their interfaces

NASA Astrophysics Data System (ADS)

Akaike, Kouki

2018-03-01

Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

Nine pairs of megastigmane enantiomers from the leaves of Eucommia ulmoides Oliver.

PubMed

Yan, Jiankun; Shi, Xuliu; Donkor, Paul Owusu; Zhu, Huajie; Gao, Xiumei; Ding, Liqin; Qiu, Feng

2017-10-01

Nine pairs of megastigmane enantiomers (1a/1b-9a/9b), comprising two new compounds (6S,9R)-blumenol C (7b), (6S,9S)-blumenol C (8b), two pairs of enantiomers (+)-(6R)-eucomegastigmane A (1a), (-)-(6S)-eucomegastigmane A (1b), (+)-(3S,4S)-eucomegastigmane B (5a), (-)-(3R,4R)-eucomegastigmane B (5b) isolated by chiral resolution firstly, and twelve known compounds, were isolated from the leaves of Eucommia ulmoides Oliver. Their structures were elucidated based on extensive spectroscopic analysis. Absolute configurations of the megastigmane enantiomers were assigned by comparing experimental ECD and OR with calculated ECD and OR. Docking-based virtual screening of all compounds showed that megastigmane enantiomers have weak intermolecular interactions with the binding site residues of angiotensin-converting enzyme (ACE) and angiotensin II type 1 receptor (AT 1 R).

Influence of Coformer Stoichiometric Ratio on Pharmaceutical Cocrystal Dissolution: Three Cocrystals of Carbamazepine/4-Aminobenzoic Acid.

PubMed

Li, Zi; Matzger, Adam J

2016-03-07

Cocrystallization is a technique to optimize solid forms that shows great potential to improve the solubility of active pharmaceutical ingredients (APIs). In some systems, an API can form cocrystals in multiple stoichiometries with the same coformer. However, it remains unclear how coformer stoichiometry influences solubility. This paper investigates the pharmaceutical:coformer pair carbamazepine (CBZ)/p-aminobenzoic acid (PABA); both CBZ/PABA 1:1 and 2:1 cocrystals are known, and a novel 4:1 CBZ/PABA cocrystal is reported here. The 4:1 cocrystal is structurally characterized, and phase stability data suggest that it is a thermodynamically unstable form. Dissolution experiments show that there is no correlation between the cocrystal stoichiometry and dissolution rate in this system. On the other hand, with the relatively weak intermolecular interactions, metastable forms can be beneficial to dissolution rate, which suggests that more effort should be devoted to cocrystal production with kinetic growth methods.

The application of CuAAC 'click' chemistry to catenane and rotaxane synthesis.

PubMed

Hänni, Kevin D; Leigh, David A

2010-04-01

The copper(I)-catalysed azide-alkyne cycloaddition (the CuAAC 'click' reaction) is proving to be a powerful new tool for the construction of mechanically interlocked molecular-level architectures. The reaction is highly selective for the functional groups involved (terminal alkynes and azides) and the experimental conditions are mild and compatible with the weak and reversible intermolecular interactions generally used to template the assembly of interlocked structures. Since the CuAAC reaction was introduced as a means of making rotaxanes by an 'active template' mechanism in 2006, it has proven effective for the synthesis of numerous different types of rotaxanes, catenanes and molecular shuttles by passive as well as active template strategies. Mechanistic insights into the CuAAC reaction itself have been provided by unexpected results encountered during the preparation of rotaxanes. In this tutorial review we highlight the rapidly increasing utility and future potential of the CuAAC reaction in mechanically interlocked molecule synthesis.

Communication: Charge-population based dispersion interactions for molecules and materials

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

Stöhr, Martin; Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching; Michelitsch, Georg S.

2016-04-21

We introduce a system-independent method to derive effective atomic C{sub 6} coefficients and polarizabilities in molecules and materials purely from charge population analysis. This enables the use of dispersion-correction schemes in electronic structure calculations without recourse to electron-density partitioning schemes and expands their applicability to semi-empirical methods and tight-binding Hamiltonians. We show that the accuracy of our method is en par with established electron-density partitioning based approaches in describing intermolecular C{sub 6} coefficients as well as dispersion energies of weakly bound molecular dimers, organic crystals, and supramolecular complexes. We showcase the utility of our approach by incorporation of the recentlymore » developed many-body dispersion method [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012)] into the semi-empirical density functional tight-binding method and propose the latter as a viable technique to study hybrid organic-inorganic interfaces.« less

Molecular recognition using receptor-free nanomechanical infrared spectroscopy based on a quantum cascade laser

PubMed Central

Kim, Seonghwan; Lee, Dongkyu; Liu, Xunchen; Van Neste, Charles; Jeon, Sangmin; Thundat, Thomas

2013-01-01

Speciation of complex mixtures of trace explosives presents a formidable challenge for sensors that rely on chemoselective interfaces due to the unspecific nature of weak intermolecular interactions. Nanomechanical infrared (IR) spectroscopy provides higher selectivity in molecular detection without using chemoselective interfaces by measuring the photothermal effect of adsorbed molecules on a thermally sensitive microcantilever. In addition, unlike conventional IR spectroscopy, the detection sensitivity is drastically enhanced by increasing the IR laser power, since the photothermal signal comes from the absorption of IR photons and nonradiative decay processes. By using a broadly tunable quantum cascade laser for the resonant excitation of molecules, we increased the detection sensitivity by one order of magnitude compared to the use of a conventional IR monochromator. Here, we demonstrate the successful speciation and quantification of picogram levels of ternary mixtures of similar explosives (trinitrotoluene (TNT), cyclotrimethylene trinitramine (RDX), and pentaerythritol tetranitrate (PETN)) using nanomechanical IR spectroscopy. PMID:23346368

Orphenadrinium picrate picric acid.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Siddaraju, B P; Yathirajan, H S; Narayana, B

2010-02-24

The asymmetric unit of the title compound N,N-dimethyl-2-[(2-methyl-phen-yl)phenyl-meth-oxy]ethanaminium picrate picric acid, C(18)H(24)NO(+)·C(6)H(2)N(3)O(7) (-)·C(6)H(3)N(3)O(7), contains one orphenadrinium cation, one picrate anion and one picric acid mol-ecule. In the orphenadrine cation, the two aromatic rings form a dihedral angle of 70.30 (7)°. There is an intra-molecular O-H⋯O hydrogen bond in the picric acid mol-ecule, which generates an S(6) ring motif. In the crystal structure, the orphenadrine cations, picrate anions and picric acid mol-ecules are connected by strong inter-molecular N-H⋯O hydrogen bonds, π⋯π inter-actions between the benzene rings of cations and anions [centroid-centroid distance = 3.5603 (9) Å] and weak C-H⋯O hydrogen bonds, forming a three-dimensional network.

Supramolecular architecture based on [Fe(CN)6]3- metallotectons and melaminium synthons

NASA Astrophysics Data System (ADS)

Krichen, Firas; Walha, Siwar; Lhoste, Jérôme; Bulou, Alain; Kabadou, Ahlem; Goutenoire, François

2017-10-01

Assembly involving [Fe(CN)6]3- metallotectons as building units and melaminium organic cation has been envisioned in order to elaborate a hybrid supramolecular based on ionic H-bonds with formula {(H-mel)4[Fe(CN)6]Cl} (H-mel+: melaminium cation). The compound has been prepared by diffusion method and characterized by single-crystal X-ray diffraction, EDX analysis, and Raman-IR spectroscopies with assignment from ab initio calculations. The melaminium exhibit self cationic coupling with cyclic hydrogen bonds to give a one dimensional {[H-mel]+}∝ synthon. Therefore, these cationic ribbons are inter-linked via hydrogen bonds by the anionic tectons [Fe(CN)6]3- and chlorine anion resulting on a 3D network. Molecular hirshfeld surfaces revealed that the crystal structure has been supported mainly by Nsbnd H⋯N and Nsbnd H⋯Cl intermolecular Hydrogen bonds and by favoured C⋯C and C⋯N weak interactions.

Detection of phosphorylation states by intermolecular sensitization of lanthanide-peptide conjugates.

PubMed

Pazos, Elena; Goličnik, Marko; Mascareñas, José L; Vázquez, M Eugenio

2012-10-04

The luminescence of a designed peptide equipped with a coordinatively-unsaturated lanthanide complex is modulated by the phosphorylation state of a serine residue in the sequence. While the phosphorylated state is weakly emissive, even in the presence of an external antenna, removal of the phosphate allows coordination of the sensitizer to the metal, yielding a highly emissive supramolecular complex.

2′-Chloro-4-meth­oxy-3-nitro­benzil

PubMed Central

Nithya, G.; Thanuja, B.; Chakkaravarthi, G.; Kanagam, Charles C.

2011-01-01

In the title compound, C15H10ClNO5, the dihedral angle between the aromatic rings is 87.99 (5)°. The O—C—C—O torsion angle between the two carbonyl units is −119.03 (16)°. The crystal structure is stabilized by a weak intermolecular C—H⋯O hydrogen bond. PMID:21754895

The Microwave Spectrum of Argon-Vinyl Chloride

NASA Astrophysics Data System (ADS)

Leung, Helen O.; Marshall, Mark D.

2011-06-01

Through the systematic comparison of the structures of a series of complexes formed between protic acid and fluorine substituted ethylenes, we have been able to observe how tuning the properties of the functional groups (F and H atoms) in ethylene using additional F atoms causes these groups to compete or cooperate with each other in intermolecular interactions. A necessary step for expanding our work in the next natural direction by examining the effects of the less electronegative, but more polarizable Cl atom is the determination of the structures of protic acid-vinyl chloride complexes. Since the rich microwave spectrum of Ar-vinyl chloride has not previously been reported, it is essential to first characterize this rare gas complex. We have observed strong b-type and weak a-type transitions for both 35Cl and 37Cl versions of this species, all of which appear to be doubled. Although ab initio calculations suggest a sufficiently large value of μ_c, c-type lines remain elusive. Indeed, these same calculations reveal the presence of several minima on the interaction potential energy surface, which may provide an explanation.

Co-Binding of Pharmaceutical Compounds at Mineral Surfaces: Molecular Investigations of Dimer Formation at Goethite/Water Interfaces.

PubMed

Xu, Jing; Marsac, Rémi; Costa, Dominique; Cheng, Wei; Wu, Feng; Boily, Jean-François; Hanna, Khalil

2017-08-01

The emergence of antibiotic and anti-inflammatory agents in aquatic and terrestrial systems is becoming a serious threat to human and animal health worldwide. Because pharmaceutical compounds rarely exist individually in nature, interactions between various compounds can have unforeseen effects on their binding to mineral surfaces. This work demonstrates this important possibility for the case of two typical antibiotic and anti-inflammatory agents (nalidixic acid (NA) and niflumic acid (NFA)) bound at goethite (α-FeOOH) used as a model mineral surface. Our multidisciplinary study, which makes use of batch sorption experiments, vibration spectroscopy and periodic density functional theory calculations, reveals enhanced binding of the otherwise weakly bound NFA caused by unforeseen intermolecular interactions with mineral-bound NA. This enhancement is ascribed to the formation of a NFA-NA dimer whose energetically favored formation (-0.5 eV compared to free molecules) is predominantly driven by van der Waals interactions. A parallel set of efforts also showed that no cobinding occurred with sulfamethoxazole (SMX) because of the lack of molecular interactions with coexisting contaminants. As such, this article raises the importance of recognizing drug cobinding, and lack of cobinding, for predicting and developing policies on the fate of complex mixtures of antibiotics and anti-inflammatory agents in nature.

Novel bimetallic thiocyanate-bridged Cu(II)-Hg(II) compounds-synthesis, X-Ray studies and magnetic properties

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

Machura, B., E-mail: basia@ich.us.edu.pl; Switlicka, A.; Zwolinski, P.

2013-01-15

Seven novel heterobimetallic Cu/Hg polymers based on thiocyanate bridges have been synthesised and characterised by means of IR, EPR, magnetic measurements and single crystal X-Ray. Three of them, [Cu(pzH){sub 4}Hg(SCN){sub 4}]{sub n} (1) [Cu(indH){sub 4}Hg(SCN){sub 4}]{sub n} (2) and [Cu(ampy){sub 2}Hg(SCN){sub 4}]{sub n} (3), have one-dimensional coordination structure. Two compounds [Cu(pzH){sub 2}Hg(SCN){sub 4}]{sub n} (4) and [Cu(abzimH)Hg(SCN){sub 4}]{sub n} (5) form two-dimensional nets, whereas the complexes [Cu(pyCN){sub 2}Hg(SCN){sub 4}]{sub n} (6) and [Cu(pyCH(OH)(OMe)){sub 2}Hg(SCN){sub 4}]{sub n} (7) are three-dimensional coordination polymers. The chains of 1 are connected by the intermolecular N-H Bullet Bullet Bullet N hydrogen bonds to the threemore » dimensional net. In 2 the N-H Bullet Bullet Bullet S hydrogen bonds link the polymeric chains to the two dimensional layer extending along crystallographic (0 0 1) plane. The polymeric chains of compound 3 are joined by the intermolecular N-H Bullet Bullet Bullet N and N-H Bullet Bullet Bullet S hydrogen bonds to the three dimensional net. The polymeric layers of 4 are connected by the intermolecular N-H Bullet Bullet Bullet N hydrogen bonds to the three dimensional net. - Graphical abstract: Novel bimetallic thiocyanate-bridged Cu(II)-Hg(II) compound-synthesis,X-Ray studies and magnetic properties. Highlights: Black-Right-Pointing-Pointer Novel heterobimetallic Cu/Hg coordination polymers were synthesised. Black-Right-Pointing-Pointer The multidimensional structures have been proved by single X-ray analysIs. Black-Right-Pointing-Pointer A variation in the crystalline architectures was observed depending on auxiliary ligands. Black-Right-Pointing-Pointer Magnetic measurements indicate weak exchange interaction between Cu(II) in the crystal lattices below 10 K.« less

Terahertz laser spectroscopy of the water dimer intermolecular vibrations. I. (D2O)2

NASA Astrophysics Data System (ADS)

Braly, L. B.; Cruzan, J. D.; Liu, K.; Fellers, R. S.; Saykally, R. J.

2000-06-01

Terahertz laser VRT spectra of the water dimer consisting of 731 transitions measured with an average precision of 2 MHz and involving four (D2O)2 intermolecular vibrations (one previously published) have been measured between 65 and 104 cm-1. The precisely determined energy level patterns differ both qualitatively and quantitatively from the predictions of several dimer potentials tested, and reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by standard normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as among different vibrations. Particularly, the 83 cm-1 (acceptor wag) and 90 cm-1 (D2O)2 (acceptor twist) vibrations interact through a Coriolis perturbation. These spectra provide the basis for our recent determination of the water pair potential. The corresponding data set for (H2O)2 is presented in an accompanying paper.

Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover

PubMed Central

McGowan, Lauren C.; Hamelberg, Donald

2013-01-01

Enzyme catalysis is central to almost all biochemical processes, speeding up rates of reactions to biological relevant timescales. Enzymes make use of a large ensemble of conformations in recognizing their substrates and stabilizing the transition states, due to the inherent dynamical nature of biomolecules. The exact role of these diverse enzyme conformations and the interplay between enzyme conformational dynamics and catalysis is, according to the literature, not well understood. Here, we use molecular dynamics simulations to study human cyclophilin A (CypA), in order to understand the role of enzyme motions in the catalytic mechanism and recognition. Cyclophilin A is a tractable model system to study using classical simulation methods, because catalysis does not involve bond formation or breakage. We show that the conformational dynamics of active site residues of substrate-bound CypA is inherent in the substrate-free enzyme. CypA interacts with its substrate via conformational selection as the configurations of the substrate changes during catalysis. We also show that, in addition to tight intermolecular hydrophobic interactions between CypA and the substrate, an intricate enzyme-substrate intermolecular hydrogen-bonding network is extremely sensitive to the configuration of the substrate. These enzyme-substrate intermolecular interactions are loosely formed when the substrate is in the reactant and product states and become well formed and reluctant to break when the substrate is in the transition state. Our results clearly suggest coupling among enzyme-substrate intermolecular interactions, the dynamics of the enzyme, and the chemical step. This study provides further insights into the mechanism of peptidyl-prolyl cis/trans isomerases and the general interplay between enzyme conformational dynamics and catalysis. PMID:23332074

Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover.

PubMed

McGowan, Lauren C; Hamelberg, Donald

2013-01-08

Enzyme catalysis is central to almost all biochemical processes, speeding up rates of reactions to biological relevant timescales. Enzymes make use of a large ensemble of conformations in recognizing their substrates and stabilizing the transition states, due to the inherent dynamical nature of biomolecules. The exact role of these diverse enzyme conformations and the interplay between enzyme conformational dynamics and catalysis is, according to the literature, not well understood. Here, we use molecular dynamics simulations to study human cyclophilin A (CypA), in order to understand the role of enzyme motions in the catalytic mechanism and recognition. Cyclophilin A is a tractable model system to study using classical simulation methods, because catalysis does not involve bond formation or breakage. We show that the conformational dynamics of active site residues of substrate-bound CypA is inherent in the substrate-free enzyme. CypA interacts with its substrate via conformational selection as the configurations of the substrate changes during catalysis. We also show that, in addition to tight intermolecular hydrophobic interactions between CypA and the substrate, an intricate enzyme-substrate intermolecular hydrogen-bonding network is extremely sensitive to the configuration of the substrate. These enzyme-substrate intermolecular interactions are loosely formed when the substrate is in the reactant and product states and become well formed and reluctant to break when the substrate is in the transition state. Our results clearly suggest coupling among enzyme-substrate intermolecular interactions, the dynamics of the enzyme, and the chemical step. This study provides further insights into the mechanism of peptidyl-prolyl cis/trans isomerases and the general interplay between enzyme conformational dynamics and catalysis. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Quantum mechanical force field for water with explicit electronic polarization.

PubMed

Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

2013-08-07

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

Biological Activity Predictions and Hydrogen Bonding Analysis in Quinolines

NASA Astrophysics Data System (ADS)

Gupta, Palvi; Kamni

The paper has been designed to make a comprehensive review of a particular series of organic molecular assembly in the form of compendium. An overview of general description of fifteen quinoline derivatives has been given. The biological activity spectra of quinoline derivatives have been correlated on structure activity relationships base which provides the different Pa (possibility of activity) and Pi (possibility of inactivity) values. Expositions of the role of intermolecular interactions in the identified derivatives have been discussed with the standard distance and angle cut-off criteria criteria as proposed by Desiraju and Steiner (1999) in an International monogram on crystallography. Distance-angle scatter plots for intermolecular interactions are presented for a better understanding of the packing interactions which exist in quinoline derivatives.

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

Factors affecting the viscosity in high concentration solutions of different monoclonal antibodies.

PubMed

Yadav, Sandeep; Shire, Steven J; Kalonia, Devendra S

2010-12-01

The viscosity profiles of four different IgG(1) molecules were studied as a function of concentration at pH 6.0. At high concentrations, MAb-H and -A showed significantly higher viscosities as compared to MAb-G and -E. Zeta Potential (ξ) measurements showed that all the IgG(1) molecules carried a net positive charge at this pH. MAb-G showed the highest positive zeta potential followed by MAb-E, -H, and -A. A consistent interpretation of the impact of net charge on viscosity for these MAbs is not possible, suggesting that electroviscous effects cannot explain the differences in viscosity. Values of k(D) (dynamic light scattering) indicated that the intermolecular interactions were repulsive for MAb-E and -G; and attractive for MAb-H and -A. Solution storage modulus (G') in high concentration solutions was consistent with attractive intermolecular interactions for MAb-H and -A, and repulsive interactions for MAb-G and -E. Effect of salt addition on solution G' and k(D) indicated that the interactions were primarily electrostatic in nature. The concentration dependent viscosity data were analyzed using a modified Ross and Minton equation. The analysis explicitly differentiates between the effect of molecular shape, size, self-crowding, and electrostatic intermolecular interactions in governing high concentration viscosity behavior. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association

Intermolecular interactions and the thermodynamic properties of supercritical fluids.

PubMed

Yigzawe, Tesfaye M; Sadus, Richard J

2013-05-21

The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.

The role of van der Waals interaction in the tilted binding of amine molecules to the Au(111) surface

NASA Astrophysics Data System (ADS)

Le, Duy; Aminpour, Maral; Kiejna, Adam; Rahman, Talat S.

2012-06-01

We present the results of ab initio electronic structure calculations for the adsorption characteristics of three amine molecules on Au(111), which show that the inclusion of van der Waals interactions between the isolated molecule and the surface leads in general to good agreement with experimental data on the binding energies. Each molecule, however, adsorbs with a small tilt angle (between -5 and 9°). For the specific case of 1,4-diaminobenzene (BDA) our calculations reproduce the larger tilt angle (close to 24°) measured by photoemission experiments, when intermolecular (van der Waals) interactions (for about 8% coverage) are included. These results point not only to the important contribution of van der Waals interactions to molecule-surface binding energy, but also that of intermolecular interactions, often considered secondary to that between the molecule and the surface, in determining the adsorption geometry and pattern formation.

MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

EPA Science Inventory

Abstract
One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

Intermolecular symmetry-adapted perturbation theory study of large organic complexes.

PubMed

Heßelmann, Andreas; Korona, Tatiana

2014-09-07

Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.

Investigation on intermolecular interaction between berberine and β-cyclodextrin by 2D UV-Vis asynchronous spectra

NASA Astrophysics Data System (ADS)

He, Anqi; Kang, Xiaoyan; Xu, Yizhuang; Noda, Isao; Ozaki, Yukihiro; Wu, Jinguang

2017-10-01

The interaction between berberine chloride and β-cyclodextrin (β-CyD) is investigated via 2D asynchronous UV-Vis spectrum. The occurrence of cross peaks around (420 nm, 420 nm) in 2D asynchronous spectrum reveals that specific intermolecular interaction indeed exists between berberine chloride and β-CyD. In spite of the difficulty caused by overlapping of cross peaks, we manage to confirm that the 420 nm band of berberine undergoes a red-shift, and its bandwidth decreases under the interaction with β-CyD. The red-shift of the 420 nm band that can be assigned to n-π* transition indicates the environment of berberine becomes more hydrophobic. The above spectral behavior is helpful in understanding why the solubility of berberine is enhanced by β-CyD.

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

PubMed

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Optical properties of azobenzene-functionalized self-assembled monolayers: Intermolecular coupling and many-body interactions

NASA Astrophysics Data System (ADS)

Cocchi, Caterina; Moldt, Thomas; Gahl, Cornelius; Weinelt, Martin; Draxl, Claudia

2016-12-01

In a joint theoretical and experimental work, the optical properties of azobenzene-functionalized self-assembled monolayers (SAMs) are studied at different molecular packing densities. Our results, based on density-functional and many-body perturbation theory, as well as on differential reflectance (DR) spectroscopy, shed light on the microscopic mechanisms ruling photo-absorption in these systems. While the optical excitations are intrinsically excitonic in nature, regardless of the molecular concentration, in densely packed SAMs intermolecular coupling and local-field effects are responsible for a sizable weakening of the exciton binding strength. Through a detailed analysis of the character of the electron-hole pairs, we show that distinct excitations involved in the photo-isomerization at low molecular concentrations are dramatically broadened by intermolecular interactions. Spectral shifts in the calculated DR spectra are in good agreement with the experimental results. Our findings represent an important step forward to rationalize the excited-state properties of these complex materials.

Pressure induced enhancement of the magnetic ordering temperature in rhenium(IV) monomers

PubMed Central

Woodall, Christopher H.; Craig, Gavin A.; Prescimone, Alessandro; Misek, Martin; Cano, Joan; Faus, Juan; Probert, Michael R.; Parsons, Simon; Moggach, Stephen; Martínez-Lillo, José; Murrie, Mark; Kamenev, Konstantin V.; Brechin, Euan K.

2016-01-01

Materials that demonstrate long-range magnetic order are synonymous with information storage and the electronics industry, with the phenomenon commonly associated with metals, metal alloys or metal oxides and sulfides. A lesser known family of magnetically ordered complexes are the monometallic compounds of highly anisotropic d-block transition metals; the ‘transformation' from isolated zero-dimensional molecule to ordered, spin-canted, three-dimensional lattice being the result of through-space interactions arising from the combination of large magnetic anisotropy and spin-delocalization from metal to ligand which induces important intermolecular contacts. Here we report the effect of pressure on two such mononuclear rhenium(IV) compounds that exhibit long-range magnetic order under ambient conditions via a spin canting mechanism, with Tc controlled by the strength of the intermolecular interactions. As these are determined by intermolecular distance, ‘squeezing' the molecules closer together generates remarkable enhancements in ordering temperatures, with a linear dependence of Tc with pressure. PMID:28000676

Mapping the force field of a hydrogen-bonded assembly

NASA Astrophysics Data System (ADS)

Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2014-05-01

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Theoretical study of optical activity of 1:1 hydrogen bond complexes of water with S-warfarin

NASA Astrophysics Data System (ADS)

Dadsetani, Mehrdad; Abdolmaleki, Ahmad; Zabardasti, Abedin

2016-11-01

The molecular interaction between S-warfarin (SW) and a single water molecule was investigated using the B3LYP method at 6-311 ++G(d,p) basis set. The vibrational spectra of the optimized complexes have been investigated for stabilization checking. Quantum theories of atoms in molecules, natural bond orbitals, molecular electrostatic potentials and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. The intermolecular charge transfer in the most stable complex is in the opposite direction from those in the other complexes. The optical spectra and the hyperpolarizabilities of SW-water hydrogen bond complexes have been computed.

Intermolecular interactions in aqueous solutions of gallic acid at 296-306 K according to spectrofluorimetry and densimetry data

NASA Astrophysics Data System (ADS)

Grigoryan, K. R.; Sargsyan, L. S.

2015-12-01

Features of intermolecular interactions in aqueous solutions of gallic acid (GA) are studied by means of densimetry and fluorescence spectroscopy (intrinsic fluorescence, 2D spectra, and excitation/ emission matrix fluorescence spectra, 3D) at 296.15, 301.15, and 306.15 K in the concentration range of 5.88 × 10-4-5.88 × 10-2 mol L-1. It is shown by analyzing the concentration and temperature dependences of the apparent molar volumes and fluorescence parameters of GA that the equilibrium between nonassociated and associated species in the solution and the hydration of these species undergo changes.

Correlational Effects of the Molecular-Tilt Configuration and the Intermolecular van der Waals Interaction on the Charge Transport in the Molecular Junction.

PubMed

Shin, Jaeho; Gu, Kyungyeol; Yang, Seunghoon; Lee, Chul-Ho; Lee, Takhee; Jang, Yun Hee; Wang, Gunuk

2018-06-25

Molecular conformation, intermolecular interaction, and electrode-molecule contacts greatly affect charge transport in molecular junctions and interfacial properties of organic devices by controlling the molecular orbital alignment. Here, we statistically investigated the charge transport in molecular junctions containing self-assembled oligophenylene molecules sandwiched between an Au probe tip and graphene according to various tip-loading forces ( F L ) that can control the molecular-tilt configuration and the van der Waals (vdW) interactions. In particular, the molecular junctions exhibited two distinct transport regimes according to the F L dependence (i.e., F L -dependent and F L -independent tunneling regimes). In addition, the charge-injection tunneling barriers at the junction interfaces are differently changed when the F L ≤ 20 nN. These features are associated to the correlation effects between the asymmetry-coupling factor (η), the molecular-tilt angle (θ), and the repulsive intermolecular vdW force ( F vdW ) on the molecular-tunneling barriers. A more-comprehensive understanding of these charge transport properties was thoroughly developed based on the density functional theory calculations in consideration of the molecular-tilt configuration and the repulsive vdW force between molecules.

Structural Insights into Amyloid Oligomers of the Parkinson Disease-related Protein α-Synuclein*

PubMed Central

Gallea, J. Ignacio; Celej, M. Soledad

2014-01-01

The presence of intraneuronal deposits mainly formed by amyloid fibrils of the presynaptic protein α-synuclein (AS) is a hallmark of Parkinson disease. Currently, neurotoxicity is attributed to prefibrillar oligomeric species rather than the insoluble aggregates, although their mechanisms of toxicity remain elusive. Structural details of the supramolecular organization of AS oligomers are critically needed to decipher the structure-toxicity relationship underlying their pathogenicity. In this study, we employed site-specific fluorescence to get a deeper insight into the internal architecture of AS oligomeric intermediates. We demonstrate that AS oligomers are ordered assemblies possessing a well defined pattern of intermolecular contacts. Some of these contacts involve regions that form the β-sheet core in the fibrillar state, although their spatial arrangement may differ in the two aggregated forms. However, even though the two termini are excluded from the fibrillar core, they are engaged in a number of intermolecular interactions within the oligomer. Therefore, substantial structural remodeling of early oligomeric interactions is essential for fibril growth. The intermolecular contacts identified in AS oligomers can serve as targets for the rational design of anti-amyloid compounds directed at preventing oligomeric interactions/reorganizations. PMID:25143382

Improving rubber concrete by waste organic sulfur compounds.

PubMed

Chou, Liang-Hisng; Lin, Chun-Nan; Lu, Chun-Ku; Lee, Cheng-Haw; Lee, Maw-Tien

2010-01-01

In this study, the use of crumb tyres as additives to concrete was investigated. For some time, researchers have been studying the physical properties of concrete to determine why the inclusion of rubber particles causes the concrete to degrade. Several methods have been developed to improve the bonding between rubber particles and cement hydration products (C-S-H) with the hope of creating a product with an improvement in mechanical strength. In this study, the crumb tyres were treated with waste organic sulfur compounds from a petroleum refining factory in order to modify their surface properties. Organic sulfur compounds with amphiphilic properties can enhance the hydrophilic properties of the rubber and increase the intermolecular interaction forces between rubber and C-S-H. In the present study, a colloid probe of C-S-H was prepared to measure these intermolecular interaction forces by utilizing an atomic force microscope. Experimental results showed that rubber particles treated with waste organic sulfur compounds became more hydrophilic. In addition, the intermolecular interaction forces increased with the adsorption of waste organic sulfur compounds on the surface of the rubber particles. The compressive, tensile and flexural strengths of concrete samples that included rubber particles treated with organic sulfur compound also increased significantly.

Spectroscopic investigation of the effect of salt on binding of tartrazine with two homologous serum albumins: quantification by use of the Debye-Hückel limiting law and observation of enthalpy-entropy compensation.

PubMed

Bolel, Priyanka; Datta, Shubhashis; Mahapatra, Niharendu; Halder, Mintu

2012-08-30

Formation of ion pair between charged molecule and protein can lead to interesting biochemical phenomena. We report the evolution of thermodynamics of the binding of tartrazine, a negatively charged azo colorant, and serum albumins with salt. The dye binds predominantly electrostatically in low buffer strengths; however, on increasing salt concentration, affinity decreases considerably. The calculated thermodynamic parameters in high salt indicate manifestation of nonelectrostatic interactions, namely, van der Waals force and hydrogen bonding. Site-marker competitive binding studies and docking simulations indicate that the dye binds with HSA in the warfarin site and with BSA at the interface of warfarin and ibuprofen binding sites. The docked poses indicate nearby amino acid positive side chains, which are possibly responsible for electrostatic interaction. Using the Debye-Hückel interionic attraction theory for binding equilibria, it is shown that, for electrostatic binding the calculated free energy change increases linearly with square root of ionic strength. Also UV-vis, fluorescence, CD data indicate a decrease of interaction with salt concentration. This study quantitatively relates how ionic strength modulates the strength of the protein-ligand electrostatic interaction. The binding enthalpy and entropy have been found to compensate one another. The enthalpy-entropy compensation (EEC), general property of weak intermolecular interactions, has been discussed.

The interaction of 2-mercaptobenzimidazole with human serum albumin as determined by spectroscopy, atomic force microscopy and molecular modeling.

PubMed

Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua

2013-04-01

The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments. Copyright © 2012 Elsevier B.V. All rights reserved.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

PubMed

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

PubMed Central

Christensen, Anders S.; Elstner, Marcus; Cui, Qiang

2015-01-01

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets. PMID:26328834

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

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

Christensen, Anders S., E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Cui, Qiang, E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Elstner, Marcus

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculatedmore » at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.« less

Visualizing the orientational dependence of an intermolecular potential

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

2016-02-01

Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.

Investigation on intermolecular interaction between berberine and β-cyclodextrin by 2D UV-Vis asynchronous spectra.

PubMed

He, Anqi; Kang, Xiaoyan; Xu, Yizhuang; Noda, Isao; Ozaki, Yukihiro; Wu, Jinguang

2017-10-05

The interaction between berberine chloride and β-cyclodextrin (β-CyD) is investigated via 2D asynchronous UV-Vis spectrum. The occurrence of cross peaks around (420nm, 420nm) in 2D asynchronous spectrum reveals that specific intermolecular interaction indeed exists between berberine chloride and β-CyD. In spite of the difficulty caused by overlapping of cross peaks, we manage to confirm that the 420nm band of berberine undergoes a red-shift, and its bandwidth decreases under the interaction with β-CyD. The red-shift of the 420nm band that can be assigned to n-π* transition indicates the environment of berberine becomes more hydrophobic. The above spectral behavior is helpful in understanding why the solubility of berberine is enhanced by β-CyD. Copyright © 2017. Published by Elsevier B.V.

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

PubMed

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

2013-11-01

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

Solute-solvent contact by intermolecular cross relaxation. I. The nature of the water-hydrophobic interface.

PubMed

Nordstierna, Lars; Yushmanov, Pavel V; Furó, István

2006-08-21

Intermolecular cross-relaxation rates between solute and solvent were measured by {1H} 19F nuclear magnetic resonance experiments in aqueous molecular solutions of ammonium perfluoro-octanoate and sodium trifluoroacetate. The experiments performed at three different magnetic fields provide frequency-dependent cross-relaxation rates which demonstrate clearly the lack of extreme narrowing for nuclear spin relaxation by diffusionally modulated intermolecular interactions. Supplemented by suitable intramolecular cross-relaxation, longitudinal relaxation, and self-diffusion data, the obtained cross-relaxation rates are evaluated within the framework of recent relaxation models and provide information about the hydrophobic hydration. In particular, water dynamics around the trifluoromethyl group in ammonium perfluoro-octanoate are more retarded than that in the smaller trifluoroacetate.

Insights into intermolecular interactions, electrostatic properties and the stability of C646 in the binding pocket of p300 histone acetyltransferase enzyme: a combined molecular dynamics and charge density study.

PubMed

Sivanandam, Magudeeswaran; Saravanan, Kandasamy; Kumaradhas, Poomani

2017-10-30

Histone acetyltransferases (HATs) and histone deacetylases (HDACs) are enzymes that exhibit an important transcription activity. Dysfunction of these enzymes may lead to different diseases including cancer, cardiovascular, and other diseases. Therefore, these enzymes are the potential target for the generation of new therapeutics. C646 is a synthetic p300 HAT inhibitor; its structural and the electrostatic properties are the paradigm to understand its activity in the active site of p300 HAT enzyme. The docked C646 molecule in the active site forms expected key intermolecular interactions with the amino acid residues Trp1436, Tyr1467, and one water molecule (W1861); and these interactions are important for acetylation reaction. When compare the active site structure of C646 with the gas-phase structure, it is confirmed that the electron density distribution of polar bonds are highly altered, when the molecule present in the active site. In the gas-phase structure of C646, a large negative regions of electrostatic potential is found at the vicinity of O(4), O(5), and O(6) atoms; whereas, the negative region of these atoms are reduced in the active site. The molecular dynamics (MD) simulation also performed, it reveals the conformational stability and the intermolecular interactions of C646 molecule in the active site of p300.

Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal structure, spectroscopy and DFT

NASA Astrophysics Data System (ADS)

Venkatesan, Perumal; Rajakannan, Venkatachalam; Venkataramanan, Natarajan S.; Ilangovan, Andivelu; Sundius, Tom; Thamotharan, Subbiah

2016-09-01

The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is characterized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations. The title compound crystallizes in centrosymmetric space group P21/c. Moreover, the crystal structure is primarily stabilized through intramolecular Nsbnd H⋯O and Osbnd H⋯O and intermolecular Nsbnd H⋯O and Csbnd H⋯O interactions along with carbonyl⋯carbonyl and Csbnd H⋯C contacts. These intermolecular interactions are analysed and quantified by using Hirshfeld surface analysis, PIXEL energy, NBO, AIM and DFT calculations. The overall lattice energies of the title and parent compounds suggest that the title compound is stabilized by a 4.5 kcal mol-1 higher energy than the parent compound. The additional stabilization force comes from the methoxy substitution on the title molecule, which is evident since the methoxy group is involved in the intermolecular Csbnd H⋯O interaction as an acceptor. The vibrational modes of the interacting groups are investigated using both experimental and theoretical FT-IR and FT-Raman spectra. The experimental and theoretical UV-Vis spectra agree well. The time dependent DFT spectra show that the ligand-to-ligand charge transfer is responsible for the intense absorbance of the compound.

Optimization of intermolecular potential parameters for the CO2/H2O mixture.

PubMed

Orozco, Gustavo A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

2014-10-02

Monte Carlo simulations in the Gibbs ensemble were used to obtain optimized intermolecular potential parameters to describe the phase behavior of the mixture CO2/H2O, over a range of temperatures and pressures relevant for carbon capture and sequestration processes. Commonly used fixed-point-charge force fields that include Lennard-Jones 12-6 (LJ) or exponential-6 (Exp-6) terms were used to describe CO2 and H2O intermolecular interactions. For force fields based on the LJ functional form, changes of the unlike interactions produced higher variations in the H2O-rich phase than in the CO2-rich phase. A major finding of the present study is that for these potentials, no combination of unlike interaction parameters is able to adequately represent properties of both phases. Changes to the partial charges of H2O were found to produce significant variations in both phases and are able to fit experimental data in both phases, at the cost of inaccuracies for the pure H2O properties. By contrast, for the Exp-6 case, optimization of a single parameter, the oxygen-oxygen unlike-pair interaction, was found sufficient to give accurate predictions of the solubilities in both phases while preserving accuracy in the pure component properties. These models are thus recommended for future molecular simulation studies of CO2/H2O mixtures.

Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers

NASA Astrophysics Data System (ADS)

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Cho, Kwang-Jin; Dolino, Drew M.; Chen, Wei; Li, Hongyang; Grant, Barry J.; Hancock, John F.; Gorfe, Alemayehu A.

2017-01-01

Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers. For validation we used mutagenesis, electron microscopy and biochemical assays under non-denaturing conditions. We show that partial disruption of a predicted interface through charge reversal mutation of apposed residues reduces oligomerization while introduction of cysteines at these positions enhanced dimerization likely through the formation of an intermolecular disulfide bond. Free energy calculations indicated that K-Ras dimerization involves direct but weak protein-protein interactions in solution, consistent with the notion that dimerization is facilitated by membrane binding. Taken together, our atomically detailed analyses provide unique mechanistic insights into K-Ras dimer formation and membrane organization as well as the conformational fluctuations and equilibrium thermodynamics underlying these processes.

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

Stiegler, Thomas; Sadus, Richard J., E-mail: rsadus@swin.edu.au

General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic propertiesmore » predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.« less

Probing Intermolecular Interactions in Binary Liquid Mixtures Using Femtosecond Laser-Induced Self-Defocusing.

PubMed

Maurya, Sandeep Kumar; Das, Dhiman; Goswami, Debabrata

2016-06-13

Photo-thermal behavior of binary liquid mixtures has been studied by high repetition rate (HRR) Z-scan technique with femtosecond laser pulses. Changes in the peak-valley difference in transmittance (ΔT P-V ) for closed aperture Z-scan experiments are indicative of thermal effects induced by HRR femtosecond laser pulses. We show such indicative results can have a far-reaching impact on molecular properties and intermolecular interactions in binary liquid mixtures. Spectroscopic parameters derived from this experimental technique show that the combined effect of physical and molecular properties of the constituent binary liquids can be related to the components of the binary liquid. © The Author(s) 2016.

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

NASA Astrophysics Data System (ADS)

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

1997-12-01

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

A molecular dynamics approach for predicting the glass transition temperature and plasticization effect in amorphous pharmaceuticals.

PubMed

Gupta, Jasmine; Nunes, Cletus; Jonnalagadda, Sriramakamal

2013-11-04

The objectives of this study were as follows: (i) To develop an in silico technique, based on molecular dynamics (MD) simulations, to predict glass transition temperatures (Tg) of amorphous pharmaceuticals. (ii) To computationally study the effect of plasticizer on Tg. (iii) To investigate the intermolecular interactions using radial distribution function (RDF). Amorphous sucrose and water were selected as the model compound and plasticizer, respectively. MD simulations were performed using COMPASS force field and isothermal-isobaric ensembles. The specific volumes of amorphous cells were computed in the temperature range of 440-265 K. The characteristic "kink" observed in volume-temperature curves, in conjunction with regression analysis, defined the Tg. The MD computed Tg values were 367 K, 352 K and 343 K for amorphous sucrose containing 0%, 3% and 5% w/w water, respectively. The MD technique thus effectively simulated the plasticization effect of water; and the corresponding Tg values were in reasonable agreement with theoretical models and literature reports. The RDF measurements revealed strong hydrogen bond interactions between sucrose hydroxyl oxygens and water oxygen. Steric effects led to weak interactions between sucrose acetal oxygens and water oxygen. MD is thus a powerful predictive tool for probing temperature and water effects on the stability of amorphous systems during drug development.

Can Csbnd H⋯Fsbnd C hydrogen bonds alter crystal packing features in the presence of Nsbnd H⋯Odbnd C hydrogen bond?

NASA Astrophysics Data System (ADS)

Yadav, Hare Ram; Choudhury, Angshuman Roy

2017-12-01

Intermolecular interactions involving organic fluorine have been the contemporary field of research in the area of organic solid state chemistry. While a group of researchers had refuted the importance of "organic fluorine" in guiding crystal structures, others have provided evidences for in favor of fluorine mediated interactions in the solid state. Many systematic studies have indicated that the "organic fluorine" is capable of offering weak hydrogen bonds through various supramolecular synthons, mostly in the absence of other stronger hydrogen bonds. Analysis of fluorine mediated interaction in the presence of strong hydrogen bonds has not been highlighted in detail. Hence a thorough structural investigation is needed to understand the role of "organic fluorine" in crystal engineering of small organic fluorinated molecules having the possibility of strong hydrogen bond formation in the solution and in the solid state. To fulfil this aim, we have synthesized a series of fluorinated amides using 3-methoxyphenylacetic acid and fluorinated anilines and studied their structural properties through single crystal and powder X-ray diffraction methods. Our results indicated that the "organic fluorine" plays a significant role in altering the packing characteristics of the molecule in building specific crystal lattices even in the presence of strong hydrogen bond.

Fibrinogen and fibrin.

PubMed

Weisel, John W

2005-01-01

Fibrinogen is a large, complex, fibrous glycoprotein with three pairs of polypeptide chains linked together by 29 disulfide bonds. It is 45 nm in length, with globular domains at each end and in the middle connected by alpha-helical coiled-coil rods. Both strongly and weakly bound calcium ions are important for maintenance of fibrinogen's structure and functions. The fibrinopeptides, which are in the central region, are cleaved by thrombin to convert soluble fibrinogen to insoluble fibrin polymer, via intermolecular interactions of the "knobs" exposed by fibrinopeptide removal with "holes" always exposed at the ends of the molecules. Fibrin monomers polymerize via these specific and tightly controlled binding interactions to make half-staggered oligomers that lengthen into protofibrils. The protofibrils aggregate laterally to make fibers, which then branch to yield a three-dimensional network-the fibrin clot-essential for hemostasis. X-ray crystallographic structures of portions of fibrinogen have provided some details on how these interactions occur. Finally, the transglutaminase, Factor XIIIa, covalently binds specific glutamine residues in one fibrin molecule to lysine residues in another via isopeptide bonds, stabilizing the clot against mechanical, chemical, and proteolytic insults. The gene regulation of fibrinogen synthesis and its assembly into multichain complexes proceed via a series of well-defined steps. Alternate splicing of two of the chains yields common variant molecular isoforms. The mechanical properties of clots, which can be quite variable, are essential to fibrin's functions in hemostasis and wound healing. The fibrinolytic system, with the zymogen plasminogen binding to fibrin together with tissue-type plasminogen activator to promote activation to the active enzyme plasmin, results in digestion of fibrin at specific lysine residues. Fibrin(ogen) also specifically binds a variety of other proteins, including fibronectin, albumin, thrombospondin, von Willebrand factor, fibulin, fibroblast growth factor-2, vascular endothelial growth factor, and interleukin-1. Studies of naturally occurring dysfibrinogenemias and variant molecules have increased our understanding of fibrinogen's functions. Fibrinogen binds to activated alphaIIbbeta3 integrin on the platelet surface, forming bridges responsible for platelet aggregation in hemostasis, and also has important adhesive and inflammatory functions through specific interactions with other cells. Fibrinogen-like domains originated early in evolution, and it is likely that their specific and tightly controlled intermolecular interactions are involved in other aspects of cellular function and developmental biology.

Acoustical Studies of L-leucine and L-asparagine in aqueous electrolyte through thermal expansion coefficient

NASA Astrophysics Data System (ADS)

Jajodia, S.; Chimankar, O. P.; Kalambe, A.; Goswami, S. G.

2012-12-01

Amino acids are the building blocks of the proteins; their study provides important information, about the behaviour of larger biomolecules such as proteins. The properties of proteins such as their structure, solubility, denaturation, etc. are greatly influenced by electrolytes. Ultrasonic velocity and density values have been used for evaluation of thermal expansion coefficient and adiabatic compressibility for ternary systems (amino acid/salt + water) namely L-leucine / L-asparagine each in 1.5 M aqueous solution of NaCl used as solvent for various concentrations and at different temperatures (298.15K - 323.15K). Present paper reports the variation of various thermoacoustical parameters such as Moelwyn-Hughes parameter (C1), Beyer's non-linearity parameter (B/A), internal pressure (Pi), fractional free volume (f), available volume (Va), repulsive exponent (n), molecular constant (r), van der Waals' constant (b), Debye temperatue (θD), etc. have been computed from the thermal expansion coefficient with the change of concentration and temperature. The variations of all these parameters have been interpreted in terms of various intermolecular interactions such as strong, weak, charge transfer, complex formation, hydrogen bonding interaction. The structure making and breaking properties of the interacting components existing in proposed ternary systems. It shows the associating and dissociating tendency of the molecules of solute in solvent.The hetromolecular interactions are present in both the ternary systems.

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.

Simple Model for the Benzene Hexafluorobenzene Interaction

DOE PAGES

Tillack, Andreas F.; Robinson, Bruce H.

2017-06-05

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions,more » and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.« less

Lattice dynamics of solid N2 with an ab initio intermolecular potential

NASA Astrophysics Data System (ADS)

Luty, T.; van der Avoird, A.; Berns, R. M.

1980-11-01

We have performed harmonic and self-consistent phonon lattice dynamics calculations for α and γ N2 crystals using an intermolecular potential from ab initio calculations. This potential contains electrostatic (multipole) interactions, up to all R-9 terms inclusive, anisotropic dispersion interactions up to all R-10 terms inclusive, and anisotropic overlap interactions caused by charge penetration and exchange between the molecules. The lattice constants, cohesion energy, the frequencies of the translational phonon modes and the Grüneisen parameters for the librational modes are in good agreement with experimental values, confirming the quality of the potential. The frequencies of the librational modes and those of the mixed modes are less well reproduced, especially at temperatures near the α-β phase transition. Probably, the self-consistent phonon method used does not fully account for the anharmonicity in the librations.

Simple Model for the Benzene Hexafluorobenzene Interaction

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

Tillack, Andreas F.; Robinson, Bruce H.

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions,more » and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.« less

Molecular Origins of Mesoscale Ordering in a Metalloamphiphile Phase

PubMed Central

2015-01-01

Controlling the assembly of soft and deformable molecular aggregates into mesoscale structures is essential for understanding and developing a broad range of processes including rare earth extraction and cleaning of water, as well as for developing materials with unique properties. By combined synchrotron small- and wide-angle X-ray scattering with large-scale atomistic molecular dynamics simulations we analyze here a metalloamphiphile–oil solution that organizes on multiple length scales. The molecules associate into aggregates, and aggregates flocculate into meso-ordered phases. Our study demonstrates that dipolar interactions, centered on the amphiphile headgroup, bridge ionic aggregate cores and drive aggregate flocculation. By identifying specific intermolecular interactions that drive mesoscale ordering in solution, we bridge two different length scales that are classically addressed separately. Our results highlight the importance of individual intermolecular interactions in driving mesoscale ordering. PMID:27163014

Effect of drug Piper nigrum on magnesium chloride at varying concentration and temperature through ultrasonic method: A thermoacoustic study

NASA Astrophysics Data System (ADS)

Nalle, Pallavi B.; Deshmukh, S. S.; Dorik, R. G.; Jadhav, K. M.

2016-12-01

The ultrasonic velocity (U), density (ρ), and viscosity (η) of an ethanolic extract of drug Piper nigrum with MgCl2 (metal ions) have been measured as a function of the number of moles n = (0.7009, 1.4018, 2.1027, 2.8036 and 3.5045) at 303.15, 308.15, 313.15 and 318.15 K temperature. Various thermoacoustic and their excess values such as adiabatic compressibilities (β), intermolecular free lengths (Lf), excess adiabatic compressibility (βE), excess intermolecular free length (?) have been computed using values of ultrasonic velocity (U), density (ρ), and viscosity (η). The excess values of ultrasonic velocity, specific acoustic impedance are positive, whereas isentropic compressibility and intermolecular free lengths are negative over the entire composition range of MgCl2 + P. nigrum which indicates the presence of specific interactions between unlike molecules. Molecular association is reflected by ultrasonic investigation. This may be interpreted due to the of complex formation. The chemical interaction may involve the association due to the solute-solvent and ion-solvent interaction and due to the formation of charge-transfer complexes, which is useful to understand the mechanism of their metabolism in living systems. The results obtained from these studies are helpful for pharmacological applications of drugs, transport of drugs across biological membranes.

Electric Field Effects on the Intermolecular Interactions in Water Whiskers: Insight from Structures, Energetics, and Properties

DOE PAGES

Bai, Yang; He, Hui-Min; Li, Ying; ...

2015-02-19

Modulation of intermolecular interactions in response to external electric fields could be fundamental to the formation of unusual forms of water, such as water whiskers. However, a detailed understanding of the nature of intermolecular interactions in such systems is lacking. In this study, we present novel theoretical results based on electron correlation calculations regarding the nature of H-bonds in water whiskers, which is revealed by studying their evolution under external electric fields with various field strengths. We find that the water whiskers consisting of 2-7 water molecules all have a chain-length dependent critical electric field. Under the critical electric field,more » the most compact chain structures are obtained, featuring very strong H-bonds, herein referred to as covalent H-bonds. In the case of a water dimer whisker, the bond length of the novel covalent H-bond shortens by 25%, the covalent bond order increases by 9 times, and accordingly the H-bond energy is strengthened by 5 times compared to the normal H-bond in a (H 2O) 2 cluster. Below the critical electric field, it is observed that with increasing field strength, H-bonding orbitals display gradual evolutions in the orbital energy, orbital ordering, and orbital nature (i.e., from typical -style orbital to unusual -style double H-bonding orbital). We also show that beyond the critical electric field, a single water whisker may disintegrate to form a loosely bound zwitterionic chain due to a relay-style proton transfer, whereas two water whiskers may undergo intermolecular cross-linking to form a quasi-two-dimensional water network. In conclusion, these results help shed new insight on the effects of electric fields on water whisker formation.« less

Structure and stability of the N-hydroxyurea dimer: Post-Hartree-Fock quantum mechanical study

NASA Astrophysics Data System (ADS)

Jabalameli, Ali; Venkatraman, Ramaiyer; Nowek, Andrzej; Sullivan, Richard H.

2000-10-01

The potential energy surface (PES) search of the N-hydroxyurea dimer was searched with second-order Møller-Plesset perturbation theory (MP2) and the 6-31G(d,p) basis set. Eight local minimum energy structures have been found. Four of them have relatively strong (ΔE˜-10 to -13 kcal/mol) intermolecular interactions and the others are moderately strongly interacting species (ΔE˜-3 to -7 kcal/mol). Final estimation of interaction energies was performed using the larger 6-311G(df,pd) and 6-311G(2df,2pd) basis sets. The predicted interaction energies are ΔE=-14.26 kcal/mol and -3.43 kcal/mol for the strongest and the weakest interacting forms of the studied complex, respectively, at the MP2/6-311G(2df,2pd)//MP2/6-31G(d,p) level of theory. The self-consistent field (SCF) interaction energy decomposition indicates the important influence of the deformation term magnitude on ΔE(SCF). The calculated electron correlation contribution to ΔE(MP2) depends on the geometry of the system and varies from -0.5 to -5 kcal/mol. The estimated influence of water on the stability (free energy of hydration) of N-hydroxyurea dimers using the self-consistent isodensity polarized continuum (SCI-PCM) model of solvation varies from ˜-11 kcal/mol to ˜-21 kcal/mol. The forms predicted to be more strongly interacting species in gas phase are less influenced by hydration than the more weakly interacting ones.

Stacking interactions of hydrogen-bridged rings – stronger than the stacking of benzene molecules.

PubMed

Blagojević, Jelena P; Zarić, Snežana D

2015-08-21

Analysis of crystal structures from the Cambridge Structural Database showed that 27% of all planar five-membered hydrogen-bridged rings, possessing only single bonds within the ring, form intermolecular stacking interactions. Interaction energy calculations show that interactions can be as strong as -4.9 kcal mol(-1), but dependent on ring structure.

A series of substituted (2E)-3-(2-fluoro-4-phenoxyphenyl)-1-phenylprop-2-en-1-ones.

PubMed

Chopra, Deepak; Mohan, T P; Vishalakshi, B; Row, T N Guru

2007-12-01

In the molecular structures of a series of substituted chalcones, namely (2E)-3-(2-fluoro-4-phenoxyphenyl)-1-phenylprop-2-en-1-one, C21H15FO2, (I), (2E)-3-(2-fluoro-4-phenoxyphenyl)-1-(4-fluorophenyl)prop-2-en-1-one, C21H14F2O2, (II), (2E)-1-(4-chlorophenyl)-3-(2-fluoro-4-phenoxyphenyl)prop-2-en-1-one, C21H14ClFO2, (III), (2E)-3-(2-fluoro-4-phenoxyphenyl)-1-(4-methylphenyl)prop-2-en-1-one, C22H17FO2, (IV), and (2E)-3-(2-fluoro-4-phenoxyphenyl)-1-(4-methoxyphenyl)prop-2-en-1-one, C22H17FO3, (V), the configuration of the keto group with respect to the olefinic double bond is s-cis. The molecules pack utilizing weak C-H...O and C-H...pi intermolecular contacts. Identical packing motifs involving C-H...O interactions, forming both chains and dimers, along with C-H...pi dimers and pi-pi aromatic interactions are observed in the fluoro, chloro and methyl derivatives.

Single-molecule dynamics in nanofabricated traps

NASA Astrophysics Data System (ADS)

Cohen, Adam

2009-03-01

The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

Computer Simulations of Polytetrafluoroethylene in the Solid State

NASA Astrophysics Data System (ADS)

Holt, D. B.; Farmer, B. L.; Eby, R. K.; Macturk, K. S.

1996-03-01

Force field parameters (Set I) for fluoropolymers were previously derived from MOPAC AM1 semiempirical data on model molecules. A second set (Set II) was derived from the AM1 results augmented by ab initio calculations. Both sets yield reasonable helical and phase II packing structures for polytetrafluoroethylene (PTFE) chains. However, Set I and Set II differ in the strength of van der Waals interactions, with Set II having deeper potential wells (order of magnitude). To differentiate which parameter set provides a better description of PTFE behavior, molecular dynamics simulations have been performed with Biosym Discover on clusters of PTFE chains which begin in a phase II packing environment. Added to the model are artificial constraints which allow the simulation of thermal expansion without having to define periodic boundary conditions for each specific temperature of interest. The preliminary dynamics simulations indicate that the intra- and intermolecular interactions provided by Set I are too weak. The degree of helical disorder and chain motion are high even at temperatures well below the phase II-phase IV transition temperature (19 C). Set II appears to yield a better description of PTFE in the solid state.

Synthesis, molecular and crystalline architectures, and properties of mononuclear cobalt(II)thiocyanates containing a symmetrical tailored diimine/an unsymmetrical bidentate Schiff base

NASA Astrophysics Data System (ADS)

Sarkar, Bhola Nath; Bhar, Kishalay; Kundu, Subhasis; Fun, Hoong-Kun; Ghosh, Barindra Kumar

2009-11-01

Two hexacoordinated mononuclear cobalt(II)thiocyanate complexes of general formula [Co(LL) 2(NCS) 2]. nH 2O [LL = 2,2'-dipyridylamine (dpa), n = 1, 1; LL = N-((pyridin-2-yl)benzylidene)benzylamine (pbba), n = 0, 2] have been prepared and characterized using microanalytical, spectroscopic and other physicochemical results. The compounds are non-electrolytes and behave as three-electron paramagnets. Structures of 1 and 2 are solved by X-ray diffraction measurements. Structural analyses show that each metal center in 1 and 2 adopts a distorted octahedral geometry with a CoN 6 chromophore ligated through four N atoms of two bidentate LL units; the hexacoordination is completed by two N atoms of terminal thiocyanates in mutual cis orientation. The mononuclear units in 1 are engaged in weak intermolecular N-H…S and C-H…S hydrogen bonds to give a 2D sheet structure, which is further stabilized by π…π interactions among the pyridine rings of dpa units. In the long-range form, two mononuclear units of 2 are locked by weak doubly C-H…S hydrogen bonds producing a dimeric unit, which packs through C-H…π interaction leading to a 2D continuum. In MeCN solutions, the compounds show a nearly reversible one-electron oxidative response corresponding to cobalt(III)-cobalt(II) couple. The complexes display intraligand 1(π-π∗) fluorescence at room temperature and intraligand 3(π-π∗) phosphorescence in glassy solutions (DMF at 77 K).

Propyl 3-oxo-2,3-dihydro-1,2-benzothia-zole-2-carboxyl-ate.

PubMed

Wang, Xiang-Hui; Yang, Jian-Xin; You, Cheng-Hang; Lin, Qiang

2011-09-01

The title compound, C(11)H(11)NO(3)S, was synthesized by the reaction of benzo[d]isothia-zol-3(2H)-one with propyl carbono-chloridate in toluene. The benzoisothiazolone ring system is approximately planar with a maximum deviation from the mean plane of 0.0226 (14) Å for the N atom. Weak inter-molecular C-H⋯O hydrogen bonding occurs in the crystal structure.

Molecular interactions in the betaine monohydrate-polyol deep eutectic solvents: Experimental and computational studies

NASA Astrophysics Data System (ADS)

Zahrina, Ida; Mulia, Kamarza; Yanuar, Arry; Nasikin, Mohammad

2018-04-01

DES (deep eutectic solvents) are a new class of ionic liquids that have excellent properties. The strength of interaction between molecules in the DES affects their properties and applications. In this work, the strength of molecular interactions between components in the betaine monohydrate salt and polyol (glycerol or/and propylene glycol) eutectic mixtures was studied by experimental and computational studies. The melting point and fusion enthalpy of the mixtures were measured using STA (Simultaneous Thermal Analyzer). The nature and strength of intermolecular interactions were observed by FT-IR and NMR spectroscopy. The molecular dynamics simulation was used to determine the number of H-bonds, percent occupancy, and radial distribution functions in the eutectic mixtures. The interaction between betaine monohydrate and polyol is following order: betaine monohydrate-glycerol-propylene glycol > betaine monohydrate-glycerol > betaine monohydrate-propylene glycol, where the latter is the eutectic mixture with the lowest stability, strength and extent of the hydrogen bonding interactions between component molecules. The presence of intra-molecular hydrogen bonding interactions, the inter-molecular hydrogen bonding interactions between betaine molecule and polyol, and also interactions between polyol and H2O of betaine monohydrate in the eutectic mixtures.

Relativistic effects in the intermolecular interaction-induced nuclear magnetic resonance parameters of xenon dimer.

PubMed

Hanni, Matti; Lantto, Perttu; Ilias, Miroslav; Jensen, Hans Jorgen Aagaard; Vaara, Juha

2007-10-28

Relativistic effects on the (129)Xe nuclear magnetic resonance shielding and (131)Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe(2) system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift delta, the anisotropy of the shielding tensor Deltasigma, and the NQC constant along the internuclear axis chi( parallel) are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Moller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for delta and Deltasigma by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for delta and Deltasigma in Xe(2). For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For chi( parallel), the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the (129)Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe(2), are in excellent agreement with the experiment for the first time.

Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.

PubMed

Jung, Young-Sang; Cai, Mengli; Clore, G Marius

2010-02-05

The solution structure of the IIA-IIB complex of the N,N'-diacetylchitobiose (Chb) transporter of the Escherichia coli phosphotransferase system has been solved by NMR. The active site His-89 of IIA(Chb) was mutated to Glu to mimic the phosphorylated state and the active site Cys-10 of IIB(Chb) was substituted by serine to prevent intermolecular disulfide bond formation. Binding is weak with a K(D) of approximately 1.3 mm. The two complementary interaction surfaces are largely hydrophobic, with the protruding active site loop (residues 9-16) of IIB(Chb) buried deep within the active site cleft formed at the interface of two adjacent subunits of the IIA(Chb) trimer. The central hydrophobic portion of the interface is surrounded by a ring of polar and charged residues that provide a relatively small number of electrostatic intermolecular interactions that serve to correctly align the two proteins. The conformation of the active site loop in unphosphorylated IIB(Chb) is inconsistent with the formation of a phosphoryl transition state intermediate because of steric hindrance, especially from the methyl group of Ala-12 of IIB(Chb). Phosphorylation of IIB(Chb) is accompanied by a conformational change within the active site loop such that its path from residues 11-13 follows a mirror-like image relative to that in the unphosphorylated state. This involves a transition of the phi/psi angles of Gly-13 from the right to left alpha-helical region, as well as smaller changes in the backbone torsion angles of Ala-12 and Met-14. The resulting active site conformation is fully compatible with the formation of the His-89-P-Cys-10 phosphoryl transition state without necessitating any change in relative translation or orientation of the two proteins within the complex.

Supramolecular architecture of 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole.3H2O: Synthesis, spectroscopic investigations, DFT computation, MD simulations and docking studies

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Smitha, M.; Sheena Mary, Y.; Armaković, Stevan; Armaković, Sanja J.; Rao, R. Sreenivasa; Suchetan, P. A.; Giri, L.; Pavithran, Rani; Van Alsenoy, C.

2017-12-01

Crystal and molecular structure of newly synthesized compound 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole (BMMBI) has been authenticated by single crystal X-ray diffraction, FT-IR, FT-Raman, 1H NMR, 13C NMR and UV-Visible spectroscopic techniques; compile both experimental and theoretical results which are performed by DFT/B3LYP/6-311++G(d,p) method at ground state in gas phase. Visualize nature and type of intermolecular interactions and crucial role of these interactions in supra-molecular architecture has been investigated by use of a set of graphical tools 3D-Hirshfeld surfaces and 2D-fingerprint plots analysis. The title compound stabilized by strong intermolecular hydrogen bonds N⋯Hsbnd O and O⋯Hsbnd O, which are envisaged by dark red spots on dnorm mapped surfaces and weak Br⋯Br contacts envisaged by red spot on dnorm mapped surface. The detailed fundamental vibrational assignments of wavenumbers were aid by with help of Potential Energy distribution (PED) analysis by using GAR2PED program and shows good agreement with experimental values. Besides frontier orbitals analysis, global reactivity descriptors, natural bond orbitals and Mullikan charges analysis were performed by same basic set at ground state in gas phase. Potential reactive sites of the title compound have been identified by ALIE, Fukui functions and MEP, which are mapped to the electron density surfaces. Stability of BMMBI have been investigated from autoxidation process and pronounced interaction with water (hydrolysis) by using bond dissociation energies (BDE) and radial distribution functions (RDF), respectively after MD simulations. In order to identify molecule's most important reactive spots we have used a combination of DFT calculations and MD simulations. Reactivity study encompassed calculations of a set of quantities such as: HOMO-LUMO gap, MEP and ALIE surfaces, Fukui functions, bond dissociation energies and radial distribution functions. To confirm the potential of title molecule in the area of pharmaceutics, we have also calculated a series of drug likeness parameters. Possibly important biological activity of BMMBI molecule was also confirmed by molecular docking study.

Novel Co(III)/Co(II) mixed valence compound [Co(bapen)Br2]2[CoBr4] (bapen = N,N‧-bis(3-aminopropyl)ethane-1,2-diamine): Synthesis, crystal structure and magnetic properties

NASA Astrophysics Data System (ADS)

Smolko, Lukáš; Černák, Juraj; Kuchár, Juraj; Miklovič, Jozef; Boča, Roman

2016-09-01

Green crystals of Co(III)/Co(II) mixed valence compound [Co(bapen)Br2]2[CoBr4] (bapen = N,N‧-bis(3-aminopropyl)ethane-1,2-diamine) were isolated from the aqueous system CoBr2 - bapen - HBr, crystallographically studied and characterized by elemental analysis and IR spectroscopy. Its ionic crystal structure is built up of [Co(bapen)Br2]+ cations and [CoBr4]2- anions. The Co(III) central atoms within the complex cations are hexacoordinated (donor set trans-N4Br2) with bromido ligands placed in the axial positions. The Co(II) atoms exhibit distorted tetrahedral coordination. Beside ionic forces weak Nsbnd H⋯Br intermolecular hydrogen bonding interactions contribute to the stability of the structure. Temperature variable magnetic measurements confirm the S = 3/2 behavior with the zero-field splitting of an intermediate strength: D/hc = 8.7 cm-1.

A new strategy of transforming pharmaceutical crystal forms.

PubMed

Tian, Jian; Dalgarno, Scott J; Atwood, Jerry L

2011-02-09

The robust nature of network materials allows them to (for example) respond to external stimuli such as pressure, temperature, light, or gas/solvent adsorption and desorption. There is difficulty in retaining long-range order in purely molecular organic solids, due to weak intermolecular interactions such as van der Waals forces. Here, we show gas-induced transformations of the well-known pharmaceuticals clarithromycin and lansoprazole. For clarithromycin, the stimulus is capable of converting the kinetic solvate and guest-free crystal forms to the commercial thermodynamically stable polymorph with a huge saving in energy cost relative to industrially employed methods. The synthesis of the marketing form of lansoprazole involves a solvate that readily decomposes and that is stirred in water, filtered, and dried intensively. Our method readily circumvents such synthetic problems and transforms the sensitive solvate to the marketed drug substance with ease. Such expedient transformations hold great implications for the pharmaceutical industry in general when considering the ease of transformation and mild conditions employed.

Influence of Coformer Stoichiometric Ratio on Pharmaceutical Cocrystal Dissolution: Three Cocrystals of Carbamazepine/4-Aminobenzoic Acid

PubMed Central

Li, Zi; Matzger, Adam J.

2016-01-01

Cocrystallization is a technique to optimize solid forms that shows great potential to improve the solubility of active pharmaceutical ingredients (APIs). In some systems, an API can form cocrystals in multiple stoichiometries with the same coformer. However, it remains unclear how coformer stoichiometry influences solubility. This paper investigates the pharmaceutical:coformer pair carbamazepine (CBZ)/p-aminobenzoic acid (PABA); both CBZ/PABA 1:1 and 2:1 cocrystals are known, and a novel 4:1 CBZ/PABA cocrystal is reported here. The 4:1 cocrystal is structurally characterized, and phase stability data suggest that it is a thermodynamically unstable form. Dissolution experiments show that there is no correlation between the cocrystal stoichiometry and dissolution rate in this system. On the other hand, with the relatively weak intermolecular interactions, metastable forms can be beneficial to dissolution rate, which suggests that more effort should be devoted to cocrystal production with kinetic growth methods. PMID:26837376

Roto-translational Raman spectra of pairs of hydrogen molecules from first principles.

PubMed

Gustafsson, Magnus; Frommhold, Lothar; Li, Xiaoping; Hunt, K L C

2009-04-28

We calculate the collision-induced, roto-translational, polarized, and depolarized Raman spectra of pairs of H(2) molecules. The Schrodinger equation of H(2)-H(2) scattering in the presence of a weak radiation field is integrated in the close-coupled scheme. This permits the accounting for the anisotropy of the intermolecular potential energy surface and thereby it includes mixing of polarizability components. The static polarizability invariants, trace and anisotropy, of two interacting H(2) molecules were obtained elsewhere [Li et al., J. Chem. Phys. 126, 214302 (2007)] from first principles. Here we report the associated spherical tensor components which, along with the potential surface, are input in the calculation of the supramolecular Raman spectra. Special attention is paid to the interferences in the wings of the rotational S(0)(0) and S(0)(1) lines of the H(2) molecule. The calculated Raman pair spectra show reasonable consistency with existing measurements of the polarized and depolarized Raman spectra of pairs of H(2) molecules.

Theoretical studies of alkyl radicals in the NaY and HY zeolites.

PubMed

Ghandi, Khashayar; Zahariev, Federico E; Wang, Yan Alexander

2005-08-18

Interplay of quantum mechanical calculations and experimental data on hyperfine coupling constants of ethyl radical in zeolites at several temperatures was engaged to study the geometries and binding energies and to predict the temperature dependence of hyperfine splitting of a series of alkyl radicals in zeolites for the first time. The main focus is on the hyperfine interaction of alkyl radicals in the NaY and HY zeolites. The hyperfine splitting for neutral free radicals and free radical cations is predicted for different zeolite environments. This information can be used to establish the nature of the muoniated alkyl radicals in the NaY and HY zeolites via muSR experiments. The muon hyperfine coupling constants of the ethane radical cation in these zeolites are very large with relatively little dependence on temperature. It was found that the intramolecular dynamics of alkyl free radicals are only weakly affected by their strong binding to zeolites. In contrast, the substrate binding has a significant effect on their intermolecular dynamics.

Ammoniated alkali fullerides (ND(3))(x)NaA(2)C(60): ammonia specific effects and superconductivity.

PubMed

Margadonna, Serena; Aslanis, Efstathios; Prassides, Kosmas

2002-08-28

The crystal structure of the superconducting (ND(3))(x)()NaA(2)C(60) (0.7 < or = x < or = 1, A= K, Rb) fullerides (T(c)= 6-15 K) has been studied by synchrotron X-ray and neutron powder diffraction. It is face-centered cubic (fcc) to low temperatures with Na(+)-ND(3) pairs residing in the octahedral interstices. These are disordered over the corners of two "interpenetrating" cubes with the Na(+) ions and the N atoms displaced by approximately 2.0 A and approximately 0.5 A from the center of the site and statically disordered over the corners of the inner and outer cube, respectively. Close contacts between the D atoms of the ND(3) molecules and electron rich 6:6 C-C bonds of neighboring C(60) units provide the signature of weak N-D.pi hydrogen-bonding interactions, which control the intermolecular packing in the crystal and may determine the unusual superconducting properties.

Microwave dielectric study of polar liquids at 298 K

NASA Astrophysics Data System (ADS)

Maharolkar, Aruna P.; Murugkar, A.; Khirade, P. W.

2018-05-01

Present paper deals with study of microwave dielectric properties like dielectric constant, viscosity, density and refractive index for the binary mixtures of Dimethylsulphoxide (DMSO) and Methanol over the entire concentration range were measured at 298K. The experimental data further used to determine the excess properties viz. excess static dielectric constant, excess molar volume, excess viscosity& derived properties viz. molar refraction&Bruggman factor. The values of excess properties further fitted with Redlich-Kister (R-K Fit) equation to calculate the binary coefficients and standard deviation. The resulting excess parameters are used to indicate the presence of intermolecular interactions and strength of intermolecular interactions between the molecules in the binary mixtures. Excess parameters indicate structure breaking factor in the mixture predominates in the system.

Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures.

PubMed

Odahara, Takayuki; Odahara, Koji

2016-04-01

Mixtures of neutral salts and polyethylene glycol are used for various purposes in biological studies. Although the effects of each component of the mixtures are theoretically well investigated, comprehension of their integrated effects remains insufficient. In this work, their roles and effects as a precipitant were clarified by studying dependence of precipitation curves on salt concentration for integral membrane protein/detergent particles of different physicochemical properties. The dependence of precipitation curves was reasonably related to intermolecular interactions among relevant molecules such as protein, detergent and polyethylene glycol by considering their physicochemical properties. The obtained relationships are useful as basic information to learn the early stage of biological macromolecular associations. Copyright © 2015 Elsevier Inc. All rights reserved.

Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

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

Karayel, A., E-mail: matchlessjimmy@163.com, E-mail: yccaoh@hotmail.com; Özbey, S.; Ayhan-Kılcıgil, G.

2015-12-15

The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

Concentration and temperature dependence of the refractive index of ethanol-water mixtures: influence of intermolecular interactions.

PubMed

Riobóo, R J; Philipp, M; Ramos, M A; Krüger, J K

2009-09-01

The temperature and concentration dependence of the refractive index, nD(x, T), in ethanol-water mixtures agrees with previous data in the ethanol-rich concentration range. The refractive index versus concentration x determined at 20 degrees C shows the expected maximum at about 41 mol% water (22 mass% water). The temperature derivative of the refractive index, dnD/dT, shows anomalies at lower water concentrations at about 10 mol% water but no anomaly at 41 mol% water. Both anomalies are related to intermolecular interactions, the one in nD seems to be due to molecular segregation and cluster formation while the origin of the second one in dnD/dT is still not clear.

Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization.

PubMed

Chamachi, Neharika G; Chakrabarty, Suman

2016-08-04

The pathological forms of prions are known to be a result of misfolding, oligomerization, and aggregation of the cellular prion. While the mechanism of misfolding and aggregation in prions has been widely studied using both experimental and computational tools, the structural and energetic characterization of the dimer form have not garnered as much attention. On one hand dimerization can be the first step toward a nucleation-like pathway to aggregation, whereas on the other hand it may also increase the conformational stability preventing self-aggregation. In this work, we have used extensive all-atom replica exchange molecular dynamics simulations of both monomer and dimer forms of a mouse prion protein to understand the structural, dynamic, and thermodynamic stability of dimeric prion as compared to the monomeric form. We show that prion proteins can dimerize spontaneously being stabilized by hydrophobic interactions as well as intermolecular hydrogen bonding and salt bridge formation. We have computed the conformational free energy landscapes for both monomer and dimer forms to compare the thermodynamic stability and misfolding pathways. We observe large conformational heterogeneity among the various modes of interactions between the monomers and the strong intermolecular interactions may lead to as high as 20% β-content. The hydrophobic regions in helix-2, surrounding coil regions, terminal regions along with the natively present β-sheet region appear to actively participate in prion-prion intermolecular interactions. Dimerization seems to considerably suppress the inherent dynamic instability observed in monomeric prions, particularly because the regions of structural frustration constitute the dimer interface. Further, we demonstrate an interesting reversible coupling between the Q160-G131 interaction (which leads to inhibition of β-sheet extension) and the G131-V161 H-bond formation.

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

PubMed

Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

2011-01-21

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.

Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins.

PubMed

Sorci, Mirco; Dassa, Bareket; Liu, Hongwei; Anand, Gaurav; Dutta, Amit K; Pietrokovski, Shmuel; Belfort, Marlene; Belfort, Georges

2013-06-18

In order to measure the intermolecular binding forces between two halves (or partners) of naturally split protein splicing elements called inteins, a novel thiol-hydrazide linker was designed and used to orient immobilized antibodies specific for each partner. Activation of the surfaces was achieved in one step, allowing direct intermolecular force measurement of the binding of the two partners of the split intein (called protein trans-splicing). Through this binding process, a whole functional intein is formed resulting in subsequent splicing. Atomic force microscopy (AFM) was used to directly measure the split intein partner binding at 1 μm/s between native (wild-type) and mixed pairs of C- and N-terminal partners of naturally occurring split inteins from three cyanobacteria. Native and mixed pairs exhibit similar binding forces within the error of the measurement technique (~52 pN). Bioinformatic sequence analysis and computational structural analysis discovered a zipper-like contact between the two partners with electrostatic and nonpolar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski's equality and demonstrated, as expected, that nonequilibrium dissipative measurements obtained here gave larger energies of interaction as compared with those for equilibrium. Hence, AFM coupled with our immobilization strategy and computational studies provides a useful analytical tool for the direct measurement of intermolecular association of split inteins and could be extended to any interacting protein pair.

Stabilization and Anomalous Hydration of Collagen Fibril under Heating

PubMed Central

Gevorkian, Sasun G.; Allahverdyan, Armen E.; Gevorgyan, David S.; Simonian, Aleksandr L.; Hu, Chin-Kun

2013-01-01

Background Type I collagen is the most common protein among higher vertebrates. It forms the basis of fibrous connective tissues (tendon, chord, skin, bones) and ensures mechanical stability and strength of these tissues. It is known, however, that separate triple-helical collagen macromolecules are unstable at physiological temperatures. We want to understand the mechanism of collagen stability at the intermolecular level. To this end, we study the collagen fibril, an intermediate level in the collagen hierarchy between triple-helical macromolecule and tendon. Methodology/Principal Finding When heating a native fibril sample, its Young’s modulus decreases in temperature range 20–58°C due to partial denaturation of triple-helices, but it is approximately constant at 58–75°C, because of stabilization by inter-molecular interactions. The stabilization temperature range 58–75°C has two further important features: here the fibril absorbs water under heating and the internal friction displays a peak. We relate these experimental findings to restructuring of collagen triple-helices in fibril. A theoretical description of the experimental results is provided via a generalization of the standard Zimm-Bragg model for the helix-coil transition. It takes into account intermolecular interactions of collagen triple-helices in fibril and describes water adsorption via the Langmuir mechanism. Conclusion/Significance We uncovered an inter-molecular mechanism that stabilizes the fibril made of unstable collagen macromolecules. This mechanism can be relevant for explaining stability of collagen. PMID:24244320

The origins of intra- and inter-molecular vibrational couplings: A case study of H{sub 2}O-Ar on full and reduced-dimensional potential energy surface

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

Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long

2016-01-07

The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H{sub 2}O–Ar, which explicitly incorporates interdependence on the intramolecular (Q{sub 1},  Q{sub 2},  Q{sub 3}) normal-mode coordinates of the H{sub 2}O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averagedmore » interaction energies for the (v{sub 1},  v{sub 2},  v{sub 3}) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H{sub 2}O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm{sup −1}, and required only 58 parameters. With the 3D PESs of H{sub 2}O–Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm{sup −1} for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H{sub 2}O in H{sub 2}O–Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings.« less

A general transformation to canonical form for potentials in pairwise interatomic interactions.

PubMed

Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

2015-06-14

A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

PubMed Central

Dodda, Leela S.

2017-01-01

Abstract The accurate calculation of protein/nucleic acid–ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements. PMID:28444340

Substitution effect on a hydroxylated chalcone: Conformational, topological and theoretical studies

NASA Astrophysics Data System (ADS)

Custodio, Jean M. F.; Vaz, Wesley F.; de Andrade, Fabiano M.; Camargo, Ademir J.; Oliveira, Guilherme R.; Napolitano, Hamilton B.

2017-05-01

The effect of substituents on two hydroxylated chalcones was studied in this work. The first chalcone, with a dimethylamine group (HY-DAC) and the second, with three methoxy groups (HY-TRI) were synthesized and crystallized from ethanol on centrosymmetric space group P21/c. The geometric parameters and supramolecular arrangement for both structures obtained from single crystal X-ray diffraction data were analyzed. The intermolecular interactions were investigated by Hirshfeld surfaces with their respective 2D plot for quantification of each type of contact. Additionally, the observed interactions were characterized by QTAIM analysis, and DFT calculations were applied for theoretical vibrational spectra, localization and quantification of frontier orbitals and potential electrostatic map. The flatness of both structures was affected by the substituents, which led to different monoclinic crystalline packing. The calculated harmonic vibrational frequencies and homo-lumo gap confirmed the stability of the structures, while intermolecular interactions were confirmed by potential electrostatic map and QTAIM analysis.

[Intermolecular hydrogen bond between protein and flavonoid and its contribution to the stability of the flavonoids].

PubMed

Fang, Ru; Leng, Xiao-jing; Wu, Xia; Li, Qi; Hao, Rui-fang; Ren, Fa-zheng; Jing, Hao

2012-01-01

The interactions between three proteins (BSA, lysozyme and myoglobin) and three flavonoids (quercetin, kaempferol and rutin) were analyzed, using three-dimensional fluorescence spectrometry in combination with UV-Vis spectrometry and Fourier transform infrared (FTIR) spectroscopy. The stabilities of unbound flavonoids and protein-bound flavonoids were compared. The correlation between the interaction and stability was analyzed. The results showed that the hydrophobic interaction was the main binding code in all proteins and flavonoids systems. However, the hydrogen bond has been involved merely in the BSA system. The stability of all three flavonoids (quercetin, kaempferol and rutin) was improved by BSA. There was a great correlation between the hydrogen bonding and the stability of the flavonoids in the presence of BSA. It suggested that the protection of BSA on the flavonoids was due to the intermolecular hydrogen bonding between BSA and flavonoid, and the stronger hydrogen bonding resulted in more protection.

A 3D network of helicates fully assembled by pi-stacking interactions.

PubMed

Vázquez, Miguel; Taglietti, Angelo; Gatteschi, Dante; Sorace, Lorenzo; Sangregorio, Claudio; González, Ana M; Maneiro, Marcelino; Pedrido, Rosa M; Bermejo, Manuel R

2003-08-07

The neutral dinuclear dihelicate [Cu2(L)2] x 2CH3CN (1) forms a unique 3D network in the solid state due to pi-stacking interactions, which are responsible for intermolecular antiferromagnetic coupling between Cu(II) ions.

An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin.

PubMed

Wade, Kristin R; Hotze, Eileen M; Kuiper, Michael J; Morton, Craig J; Parker, Michael W; Tweten, Rodney K

2015-02-17

β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼ 19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT.

Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions.

PubMed

Edison, John R; Spencer, Ryan K; Butterfoss, Glenn L; Hudson, Benjamin C; Hochbaum, Allon I; Paravastu, Anant K; Zuckermann, Ronald N; Whitelam, Stephen

2018-05-29

The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural sequence-specific peptoid polymers. Nanosheets exist because individual polymers can be linear and untwisted, by virtue of polymer backbone elements adopting alternating rotational states whose twists oppose and cancel. Using molecular dynamics and quantum mechanical simulations, together with experimental data, we explore the design space of flat nanostructures built from peptoids. We show that several sets of peptoid backbone conformations are consistent with their being linear, but the specific combination observed in experiment is determined by a combination of backbone energetics and the interactions made within the nanosheet. Our results provide a molecular model of the peptoid nanosheet consistent with all available experimental data and show that its structure results from a combination of intra- and intermolecular interactions.

An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin

PubMed Central

Wade, Kristin R.; Hotze, Eileen M.; Kuiper, Michael J.; Morton, Craig J.; Parker, Michael W.; Tweten, Rodney K.

2015-01-01

β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT. PMID:25646411

Nature and potency interactions of the hydrogen bond through the NBO analysis for charge transfer complex between 2-amino-4-hydroxy-6-methylpyrimidine and 2,3-pyrazinedicarboxylic acid

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Afroz, Ziya; Alam, Mohammad Jane; Bhat, Sheeraz Ahmad; Ahmad, Shabbir; Ahmad, Afaq

2018-05-01

The intermolecular interactions in complex formation between 2-amino-4-hydroxy-6-methylpyrimidine (AHMP) and 2,3-pyrazinedicarboxylicacid (PDCA) have been explored using density functional theory calculations. The isolated 1:1 molecular geometry of proton transfer (PT) complex between AHMP and PDCA has been optimized on a counterpoise corrected potential energy surface (PES) at DFT-B3LYP/6-31G(d,p) level of theory in the gaseous phase. Further, the formation of hydrogen bonded charge transfer (HBCT) complex between PDCA and AHMP has been also discussed. PT energy barrier between two extremes is calculated using potential energy surface (PES) scan by varying bond length. The intermolecular interactions have been analyzed from theoretical perspective of natural bond orbital (NBO) analysis. In addition, the interaction energy between molecular fragments involved in the complex formation has been also computed by counterpoise procedure at same level of theory.

Oxidative stress–induced assembly of PML nuclear bodies controls sumoylation of partner proteins

PubMed Central

Sahin, Umut; Ferhi, Omar; Jeanne, Marion; Benhenda, Shirine; Berthier, Caroline; Jollivet, Florence; Niwa-Kawakita, Michiko; Faklaris, Orestis; Setterblad, Niclas; Lallemand-Breitenbach, Valérie

2014-01-01

The promyelocytic leukemia (PML) protein organizes PML nuclear bodies (NBs), which are stress-responsive domains where many partner proteins accumulate. Here, we clarify the basis for NB formation and identify stress-induced partner sumoylation as the primary NB function. NB nucleation does not rely primarily on intermolecular interactions between the PML SUMO-interacting motif (SIM) and SUMO, but instead results from oxidation-mediated PML multimerization. Oxidized PML spherical meshes recruit UBC9, which enhances PML sumoylation, allow partner recruitment through SIM interactions, and ultimately enhance partner sumoylation. Intermolecular SUMO–SIM interactions then enforce partner sequestration within the NB inner core. Accordingly, oxidative stress enhances NB formation and global sumoylation in vivo. Some NB-associated sumoylated partners also become polyubiquitinated by RNF4, precipitating their proteasomal degradation. As several partners are protein-modifying enzymes, NBs could act as sensors that facilitate and confer oxidative stress sensitivity not only to sumoylation but also to other post-translational modifications, thereby explaining alterations of stress response upon PML or NB loss. PMID:24637324

Mechanisms underlying changes in indomethacin solubility with local anesthetics and related basic additives

NASA Astrophysics Data System (ADS)

Shimada, Yohsuke; Tateuchi, Ryo; Chatani, Hitoshi; Goto, Satoru

2018-03-01

Indomethacin (IND), an acidic nonsteroidal anti-inflammatory drug, and lidocaine (LID), a local anesthetic (LA), form a eutectic complex when mixed, with a lower melting point. The aqueous solubility of the mixture is greater than that of IND or LID alone, improving the bioavailability of IND. Therefore, IND and LID can be used to model changes in efficacy caused by physicochemical interactions between drugs. In this study, the intermolecular interactions between IND and structurally similar LAs were examined by measuring solubility and analyzing thermodynamics using differential scanning calorimetry. The results indicate that the solubility of IND (log S'IND) varies with LA hydrophobicity. Reductions in melting point resulting from mixing IND and LAs contributed to changes in IND solubility, attributable to direct intermolecular interactions between IND and the LAs. In addition, binding energy of IND-LA as in water was calculated, and the values were correlating with the solubility of IND in experiments. Understanding these interactions will help address some of the problems encountered in polypharmacy.

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Terahertz laser spectroscopy of the water dimer intermolecular vibrations. I. (D{sub 2}O){sub 2}

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

Braly, L. B.; Cruzan, J. D.; Liu, K.

Terahertz laser VRT spectra of the water dimer consisting of 731 transitions measured with an average precision of 2 MHz and involving four (D{sub 2}O){sub 2} intermolecular vibrations (one previously published) have been measured between 65 and 104 cm{sup -1}. The precisely determined energy level patterns differ both qualitatively and quantitatively from the predictions of several dimer potentials tested, and reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by standard normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as among different vibrations. Particularly, themore » 83 cm{sup -1} (acceptor wag) and 90 cm{sup -1} (D{sub 2}O){sub 2} (acceptor twist) vibrations interact through a Coriolis perturbation. These spectra provide the basis for our recent determination of the water pair potential. The corresponding data set for (H{sub 2}O){sub 2} is presented in an accompanying paper. (c) 2000 American Institute of Physics.« less

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

PubMed

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

2016-05-20

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

1,5-Bis[(E)-cyclo-pentyl-idene]thio-carbono-hydrazide.

PubMed

Guo, Qingliang; Sun, Junshan; Li, Jikun; Wu, Rentao; Duan, Wenzeng

2009-03-25

In the title mol-ecule, C(11)H(18)N(4)S, an intra-molecular N-H⋯N hydrogen bond [N⋯N = 2.558 (3)Å] is observed. The two cyclo-pentyl rings are disordered between two conformations in 1:1 and 2:1 ratios. In the crystal structure, weak inter-molecular N-H⋯S hydrogen bonds [N⋯S = 3.547 (3) Å] link pairs of mol-ecules into centrosymmetric dimers.

DEVELOPMENT OF A MODEL THAT CONTAINS BOTH MULTIPOLE MOMENTS AND GAUSSIANS FOR THE CALCULATION OF MOLECULAR ELECTROSTATIC POTENTIALS

EPA Science Inventory

The electrostatic interaction is a critical component of intermolecular interactions in biological processes. Rapid methods for the computation and characterization of the molecular electrostatic potential (MEP) that segment the molecular charge distribution and replace this cont...

Investigation of TNB/NNAP cocrystal synthesis, molecular interaction and formation process

NASA Astrophysics Data System (ADS)

Chen, Peng-Yuan; Zhang, Lin; Zhu, Shun-Guan; Cheng, Guang-Bin; Li, Ning-Rui

2017-01-01

A novel cocrystal of 1,3,5-trinitrobenzene (TNB) and 1-nitronaphthalene (NNAP) was synthesized by solution and mechanochemical method, respectively. The crystal structure was characterized by single crystal X-ray diffraction (SXRD). Then the intermolecular interaction was illustrated quantitatively by Hirshfeld surface analysis accordingly. Two other isostructural cocrystals, TNT (2,4,6-trinitrotoluene)/NNAP and TNP (2,4,6-trinitrophenol)/NNAP were also calculated for comparison. Among the three cocrystals, TNB/NNAP cocrystal has the largest proportion of π-π stacking interaction (12.7%). While TNP/NNAP cocrystal has a greater percentage of hydrogen bonding than the other two cocrystals, which is 43.2% of the total interactions. These results indicate electronic effect has an influence on the intermolecular interaction in the cocrystal. The IR spectra of the intermediate products provide more information about the formation process of hydrogen bonding and π-π stacking. We can tell from the differential scanning calorimetry (DSC) thermograms that a eutectic mixture was generated first after TNB and NNAP were physically mixed without grinding, and then turned into the cocrystal and finally transformed completely.

Phenyl-β-D-glucopyranoside and Phenyl-β-D-galactopyranoside dimers: Small Structural differences but Very Different Interactions

NASA Astrophysics Data System (ADS)

Usabiaga, Imanol; Camiruaga, Ander; Insausti, Aran; Çarçabal, Pierre; Cocinero, Emilio J.; León, Iker; Fernández, José A.

2018-02-01

We report a combination of laser spectroscopy in molecular jets and quantum mechanical calculations to characterize the aggregation preferences of phenyl-β-D-glucopyranoside (β-PhGlc) and phenyl-β-D-galactopyranoside (β-PhGal) homodimers. At least two structures of β-PhGlc dimer were found maintaining the same intramolecular interactions of the monomers, but with additional intermolecular interactions between the hydroxyl groups. Several isomers were also found for the dimer of β-PhGal forming extensive hydrogen bond networks between the interacting molecules, of very different shape. All the species found present several CH•••Pi and OH•••Pi interactions that add stability to the aggregates. The results show how even the smallest change in a substituent, from axial to equatorial position, plays a decisive role in the formation of the dimers. These conclusions reinforce the idea that the small structural changes between sugar units are amplified by formation of intra and intermolecular hydrogen bond networks, helping other molecules (proteins, receptors) to easily read the sugar code of glycans.

Diazo Esters as Dienophiles in Intramolecular (4 + 2) Cycloadditions: Computational Explorations of Mechanism.

PubMed

Duan, Abing; Yu, Peiyuan; Liu, Fang; Qiu, Huang; Gu, Feng Long; Doyle, Michael P; Houk, K N

2017-02-22

The first experimental examples of Diels-Alder (DA) reactions of diazo compounds as heterodienophiles with dienes have been studied with density functional theory (DFT) using the M06-2X functional. For comparison, the reactivities of diazo esters as dienophiles or 1,3-dipoles with 1,3-dienes in intermolecular model systems have been analyzed by the distortion/interaction model. The 1,3-dipolar cycloaddition is strongly favored for the intermolecular system. The intramolecular example is unique because the tether strongly favors the (4 + 2) cycloaddition.

Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies.

PubMed

Anda, André; De Vico, Luca; Hansen, Thorsten

2017-06-08

Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.

Thz Spectroscopy and DFT Modeling of Intermolecular Vibrations in Hydrophobic Amino Acids

NASA Astrophysics Data System (ADS)

Williams, michael R. C.; Aschaffenburg, Daniel J.; Schmuttenmaer, Charles A.

2013-06-01

Vibrations that involve intermolecular displacements occur in molecular crystals at frequencies in the 0.5-5 THz range (˜15-165 cm^{-1}), and these motions are direct indicators of the interaction potential between the molecules. The intermolecular potential energy surface of crystalline hydrophobic amino acids is inherently interesting simply because of the wide variety of forces (electrostatic, dipole-dipole, hydrogen-bonding, van der Waals) that are present. Furthermore, an understanding of these particular interactions is immediately relevant to important topics like protein conformation and pharmaceutical polymorphism. We measured the low-frequency absorption spectra of several polycrystalline hydrophobic amino acids using THz time-domain spectroscopy, and in addition we carried out DFT calculations using periodic boundary conditions and an exchange-correlation functional that accounts for van der Waals dispersion forces. We chose to investigate a series of similar amino acids with closely analogous unit cells (leucine, isoleucine, and allo-isoleucine, in racemic or pseudo-racemic mixtures). This allows us to consider trends in the vibrational spectra as a function of small changes in molecular arrangement and/or crystal geometry. In this way, we gain confidence that peak assignments are not based on serendipitous similarities between calculated and observed features.

High-energy, stable and recycled molecular solar thermal storage materials using AZO/graphene hybrids by optimizing hydrogen bonds.

PubMed

Luo, Wen; Feng, Yiyu; Qin, Chengqun; Li, Man; Li, Shipei; Cao, Chen; Long, Peng; Liu, Enzuo; Hu, Wenping; Yoshino, Katsumi; Feng, Wei

2015-10-21

An important method for establishing a high-energy, stable and recycled molecular solar heat system is by designing and preparing novel photo-isomerizable molecules with a high enthalpy and a long thermal life by controlling molecular interactions. A meta- and ortho-bis-substituted azobenzene chromophore (AZO) is covalently grafted onto reduced graphene oxide (RGO) for solar thermal storage materials. High grafting degree and close-packed molecules enable intermolecular hydrogen bonds (H-bonds) for both trans-(E) and cis-(Z) isomers of AZO on the surface of nanosheets, resulting in a dramatic increase in enthalpy and lifetime. The metastable Z-form of AZO on RGO is thermally stabilized with a half-life of 52 days by steric hindrance and intermolecular H-bonds calculated using density functional theory (DFT). The AZO-RGO fuel shows a high storage capacity of 138 Wh kg(-1) by optimizing intermolecular H-bonds with a good cycling stability for 50 cycles induced by visible light at 520 nm. Our work opens up a new method for making advanced molecular solar thermal storage materials by tuning molecular interactions on a nano-template.

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

PubMed

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

2009-01-13

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

Production of anti-amoxicillin ScFv antibody and simulation studying its molecular recognition mechanism for penicillins.

PubMed

Liu, Jing; Zhang, Hui C; Duan, Chang F; Dong, Jun; Zhao, Guo X; Wang, Jian P; Li, Nan; Liu, Jin Z; Li, Yu W

2016-11-01

The molecular recognition mechanism of an antibody for its hapten is very interesting. The objective of this research was to study the intermolecular interactions of an anti-amoxicillin antibody with penicillin drugs. The single chain variable fragment (ScFv) antibody was generated from a hybridoma cell strain excreting the monoclonal antibody for amoxicillin. The recombinant ScFv antibody showed similar recognition ability for penicillins to its parental monoclonal antibody: simultaneous recognizing 11 penicillins with cross-reactivities of 18-107%. The three-dimensional structure of the ScFv antibody was simulated by using homology modeling, and its intermolecular interactions with 11 penicillins were studied by using molecular docking. Results showed that three CDRs are involved in antibody recognition; CDR L3 Arg 100, CDR H3 Tyr226, and CDR H3 Arg 228 were the key contact amino acid residues; hydrogen bonding was the main antibody-drug intermolecular force; and the core structure of penicillin drugs was the main antibody binding position. These results could explain the recognition mechanism of anti-amoxicillin antibody for amoxicillin and its analogs. This is the first study reporting the production of ScFv antibody for penicillins and stimulation studying its recognition mechanism.

Dissipative exciton transfer in donor-bridge-acceptor systems: numerical renormalization group calculation of equilibrium properties.

PubMed

Tornow, Sabine; Tong, Ning-Hua; Bulla, Ralf

2006-07-05

We present a detailed model study of exciton transfer processes in donor-bridge-acceptor (DBA) systems. Using a model which includes the intermolecular Coulomb interaction and the coupling to a dissipative environment we calculate the phase diagram, the absorption spectrum as well as dynamic equilibrium properties with the numerical renormalization group. This method is non-perturbative and therefore allows one to cover the full parameter space, especially the case when the intermolecular Coulomb interaction is of the same order as the coupling to the environment and perturbation theory cannot be applied. For DBA systems with up to six sites we found a transition to the localized phase (self-trapping) depending on the coupling to the dissipative environment. We discuss various criteria which favour delocalized exciton transfer.

An Observation of Diamond-Shaped Particle Structure in a Soya Phosphatidylcohline and Bacteriorhodopsin Composite Langmuir Blodgett Film Fabricated by Multilayer Molecular Thin Film Method

NASA Astrophysics Data System (ADS)

Tsujiuchi, Y.; Makino, Y.

A composite film of soya phosphatidylcohline (soya PC) and bacteriorhodopsin (BR) was fabricated by the multilayer molecular thin film method using fatty acid and lipid on a quartz substrate. Direct Force Microscopy (DFM), UV absorption spectra and IR absorption spectra of the film were characterized on the detail of surface structure of the film. The DFM data revealed that many rhombus (diamond-shaped) particles were observed in the film. The spectroscopic data exhibited the yield of M-intermediate of BR in the film. On our modelling of molecular configuration indicate that the coexistence of the strong inter-molecular interaction and the strong inter-molecular interaction between BR trimmers attributed to form the particles.

Crystal structure of fac-[2-(4-methyl-5-phenyl-pyridin-2-yl)phenyl-κ2C1,N]bis-[2-(pyridin-2-yl)phenyl-κ2C1,N]iridium(III).

PubMed

Lee, Chi-Heon; Moon, Suk-Hee; Park, Ki-Min; Kang, Youngjin

2016-12-01

In the title compound, [Ir(C 11 H 8 N) 2 (C 18 H 14 N)], the Ir III ion adopts a distorted octa-hedral coordination environment defined by three C , N -chelating ligands, one stemming from a 2-(4-phenyl-5-methyl-pyridin-2-yl)phenyl ligand and two from 2-(pyridin-2-yl)phenyl ligands, arranged in a facial manner. The Ir III ion lies almost in the equatorial plane [deviation = 0.0069 (15) Å]. In the crystal, inter-molecular π-π stacking inter-actions, as well as inter-molecular C-H⋯π inter-actions, are present, leading to a three-dimensional network.

Energy transfer dynamics and kinetics of elementary processes (promoted) by gas-phase CO2 -N2 collisions: Selectivity control by the anisotropy of the interaction.

PubMed

Lombardi, Andrea; Pirani, Fernando; Laganà, Antonio; Bartolomei, Massimiliano

2016-06-15

In this work, we exploit a new formulation of the potential energy and of the related computational procedures, which embodies the coupling between the intra and intermolecular components, to characterize possible propensities of the collision dynamics in energy transfer processes of interest for simulation and control of phenomena occurring in a variety of equilibrium and nonequilibrium environments. The investigation reported in the paper focuses on the prototype CO2 -N2 system, whose intramolecular component of the interaction is modeled in terms of a many body expansion while the intermolecular component is modeled in terms of a recently developed bonds-as-interacting-molecular-centers' approach. The main advantage of this formulation of the potential energy surface is that of being (a) truly full dimensional (i.e., all the variations of the coordinates associated with the molecular vibrations and rotations on the geometrical and electronic structure of the monomers, are explicitly taken into account without freezing any bonds or angles), (b) more flexible than other usual formulations of the interaction and (c) well suited for fitting procedures better adhering to accurate ab initio data and sensitive to experimental arrangement dependent information. Specific attention has been given to the fact that a variation of vibrational and rotational energy has a higher (both qualitative and quantitative) impact on the energy transfer when a more accurate formulation of the intermolecular interaction (with respect to that obtained when using rigid monomers) is adopted. This makes the potential energy surface better suited for the kinetic modeling of gaseous mixtures in plasma, combustion and atmospheric chemistry computational applications. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Cooperativity effect involving drug-DNA/RNA intermolecular interaction: A B3LYP-D3 and MP2 theoretical investigation on ketoprofen⋯cytosine⋯H2O system.

PubMed

Zhen, Jun-Ping; Wei, Xiao-Chun; Shi, Wen-Jing; Huang, Zhu-Yuan; Jin, Bo; Zhou, Yu-Kun

2017-11-14

In order to examine the origin of the drug action and design new DNA/RNA-targeted drugs, the cooperativity effect involving drug-DNA/RNA intermolecular interaction in ketoprofen⋯cytosine⋯H 2 O ternary system were investigated by the B3LYP, B3LYP-D3, and MP2 methods with the 6-311++G(2d,p) basis set. The thermodynamic cooperativity was also evaluated at 310.15 K. The N-H⋯O, O-H⋯O, O-H⋯N, C-H⋯N, and C-H⋯O H bonds coexist in ternary complexes. The intermolecular interactions obtained by B3LYP-D3 are close to those calculated by MP2. The steric effects and van der Waals interactions have little influence on the cooperativity effects. The anti-cooperativity effect in ket⋯cyt⋯H 2 O is far more notable than the cooperativity effect, and the stability of the cyclic structure with anti-cooperativity effect is higher than that of the linear structure with cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that, in the presence of H 2 O, the anti-cooperativity effect plays a dominant role in the drug-DNA/RNA interaction, and the nature of the hydration in the binding of drugs to DNA/RNA bases is the H-bonding anti-cooperativity effect. Furthermore, the drug always links simultaneously with DNA/RNA base and H 2 O, and only in this way can the biological activity of drugs play a role. In most cases, the enthalpy change is the major factor driving the cooperativity, as is different from most of biomacromolecule complexes.

Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions.

PubMed

Ganguly, Debabani; Chen, Jianhan

2011-04-01

Coupled binding and folding is frequently involved in specific recognition of so-called intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a lack of stable tertiary fold for function. Here, we exploit topology-based Gō-like modeling as an effective tool for the mechanism of IDP recognition within the theoretical framework of minimally frustrated energy landscape. Importantly, substantial differences exist between IDPs and globular proteins in both amino acid sequence and binding interface characteristics. We demonstrate that established Gō-like models designed for folded proteins tend to over-estimate the level of residual structures in unbound IDPs, whereas under-estimating the strength of intermolecular interactions. Such systematic biases have important consequences in the predicted mechanism of interaction. A strategy is proposed to recalibrate topology-derived models to balance intrinsic folding propensities and intermolecular interactions, based on experimental knowledge of the overall residual structure level and binding affinity. Applied to pKID/KIX, the calibrated Gō-like model predicts a dominant multistep sequential pathway for binding-induced folding of pKID that is initiated by KIX binding via the C-terminus in disordered conformations, followed by binding and folding of the rest of C-terminal helix and finally the N-terminal helix. This novel mechanism is consistent with key observations derived from a recent NMR titration and relaxation dispersion study and provides a molecular-level interpretation of kinetic rates derived from dispersion curve analysis. These case studies provide important insight into the applicability and potential pitfalls of topology-based modeling for studying IDP folding and interaction in general. Copyright © 2011 Wiley-Liss, Inc.

Investigating Intermolecular Interactions via Scanning Tunneling Microscopy: An Experiment for the Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Pullman, David; Peterson, Karen I.

2004-01-01

A scanning tunneling microscope (STM) project designed as a module for the undergraduate physical chemistry laboratory is described. The effects of van der Waals interactions on the condensed-phase structure are examined by the analysis of the pattern of the monolayer structures.

Implications of hydrogen/halogen-bond in the stabilization of confined water and anion-water clusters by a cationic receptor

NASA Astrophysics Data System (ADS)

Hoque, Md. Najbul; Das, Gopal

2016-03-01

Anion complexation of benzene capped flexible tripodal receptor and solid state stabilization of discrete hybrid anion-water or infinite water clusters by various supramolecular interactions are reported here. The crystal structure of the receptor in protonated states shows all the three arms projected in one direction. We structurally demonstrate discrete fluoride-water cluster [F2-H2O]2- and square shaped chloride-water cluster [Cl2-(H2O)2]2- inside the cationic channel of the receptor. Structural analysis also reveals that these clusters are stabilized inside the channel through active participation of N/C/Ow‧H⋯Ow, N/C/Ow‧H⋯X- (X- = F-, Cl- and I-) H-bonds and electrostatic interactions. Moreover, C-H⋯π and π⋯π types weak intermolecular interactions appear to play crucial role in supramolecular assembly of receptor. Additionally, on treatment with hydroiodic acid (HI) L resulted zwitterionic iodide complex. Crystal structure reveals the presence of S···I halogen bonded dimer, I2···I halogen bond, 1D infinite water chain and neutral iodine molecules. It is comprehensible that ligand basal structure (benzene capped and N-bridge head in two tripodal) play crucial roles in the formation of diverse halide-water cluster. All structures were well examined by different techniques such as NMR, IR, TGA, DSC, PXRD and XRD.

Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations

PubMed Central

2017-01-01

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy. PMID:28783431

Nanoparticles in ionic liquids: interactions and organization.

PubMed

He, Zhiqi; Alexandridis, Paschalis

2015-07-28

Ionic liquids (ILs), defined as low-melting organic salts, are a novel class of compounds with unique properties and a combinatorially great chemical diversity. Ionic liquids are utilized as synthesis and dispersion media for nanoparticles as well as for surface functionalization. Ionic liquid and nanoparticle hybrid systems are governed by a combined effect of several intermolecular interactions between their constituents. For each interaction, including van der Waals, electrostatic, structural, solvophobic, steric, and hydrogen bonding, the characterization and quantitative calculation methods together with factors affecting these interactions are reviewed here. Various self-organized structures based on nanoparticles in ionic liquids are generated as a result of a balance of these intermolecular interactions. These structures, including colloidal glasses and gels, lyotropic liquid crystals, nanoparticle-stabilized ionic liquid-containing emulsions, ionic liquid surface-functionalized nanoparticles, and nanoscale ionic materials, possess properties of both ionic liquids and nanoparticles, which render them useful as novel materials especially in electrochemical and catalysis applications. This review of the interactions within nanoparticle dispersions in ionic liquids and of the structure of nanoparticle and ionic liquid hybrids provides guidance on the rational design of novel ionic liquid-based materials, enabling applications in broad areas.

Molecular Self-Assembly Driven by London Dispersion Forces

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

Li, Guo; Cooper, Valentino R; Cho, Jun-Hyung

2011-01-01

The nature and strength of intermolecular interactions are crucial to a variety of kinetic and dynamic processes at surfaces. Whereas strong chemisorption bonds are known to facilitate molecular binding, the importance of the weaker yet ubiquitous van der Waals (vdW) interactions remains elusive in most cases. Here we use first-principles calculations combined with kinetic Monte Carlo simulations to unambiguously demonstrate the vital role that vdW interactions play in molecular self-assembly, using styrene nanowire growth on silicon as a prototypical example. We find that, only when the London dispersion forces are included, accounting for the attractive parts of vdW interactions, canmore » the effective intermolecular interaction be reversed from being repulsive to attractive. Such attractive interactions, in turn, ensure the preferred growth of long wires under physically realistic conditions as observed experimentally. We further propose a cooperative scheme, invoking the application of an electric field and the selective creation of Si dangling bonds, to drastically improve the ordered arrangement of the molecular structures. The present study represents a significant step forward in the fundamental understanding and precise control of molecular self-assembly guided by London dispersion forces.« less

Csbnd H⋯Ni and Csbnd H⋯π(chelate) interactions in nickel(II) complexes involving functionalized dithiocarbamates and triphenylphosphine

NASA Astrophysics Data System (ADS)

Sathiyaraj, E.; Thirumaran, S.; Selvanayagam, S.; Sridhar, B.; Ciattini, Samuele

2018-05-01

New bis(N-benzyl-N-substituted benzyldithiocarbamato-S,S‧)nickel(II) (1-3) and (N-benzyl-N-substituted benzyldithiocarbamato-S,S‧)(isothiocyanato-N)- (triphenylphosphane)nickel(II) (4-6) [where substituted benzyl = 2-HOsbnd C6H4sbnd CH2sbnd (1,4), 3-HOsbnd C6H4sbnd CH2sbnd (2,5), 4-Fsbnd C6H4sbnd CH2sbnd (3,6)] were synthesized and characterized using IR, electronic, and NMR (1H and 13C) spectra. X-ray structural analysis of homoleptic complex (1) and heteroleptic complexes (5 and 6) confirmed the presence of four coordinated nickel in a distorted square planar arrangement with NiS4 and NiS2PN chromophores, respectively. The νC-S stretching vibrations are observed around 990 cm-1 without any splitting supporting the bidentate coordination of the dithiocarbamate ligand. Electronic spectral studies of all the complexes (1-6) indicate that the geometry of the nickel atom is probably square planar. NMR spectra of all homoleptic and heteroleptic complexes (1-6) reveal a weak signal associated with the backbone carbon (N13CS2) in the region 204.0-210.0 ppm with a weak intensity characteristic of the quaternary carbon signals. The greater trans influence of triphenylphosphine in complexes 5 and 6 is supported by the long Nisbnd S distance compared to other Nisbnd S distance which is opposite to the NCS- ligand. In the structure of complex 5, C-H⋯π(chelate) interactions results in polymeric chain. Both structures show intramolecular Ni⋯H interactions but that on 6 is the strongest. C-H⋯π interactions are also found in 1, 5 and 6. Hirshfeld surface analysis and the associated 2D fingerprint plots of 1, 5 and 6 have been studied to evaluate intermolecular interactions. The molecular geometries of complexes 1, 5 and 6 have been optimized by abinitio HF method using LANL2DZ program.

Temperature Dependence in the Terahertz Spectrum of Nicotinamide: Anharmonicity and Hydrogen-Bonded Network.

PubMed

Takahashi, Masae; Okamura, Nubuyuki; Fan, Xinyi; Shirakawa, Hitoshi; Minamide, Hiroaki

2017-04-06

We have investigated the terahertz-spectral property of nicotinamide focusing on the temperature dependence in the range of 14-300 K. We observed that almost all peaks in the terahertz spectrum of the nicotinamide crystal showed a remarkable shift with temperature, whereas the lowest-frequency peak at 34.8 cm -1 showed a negligible shift with temperature. By analyzing the terahertz spectrum with the dispersion-corrected density functional theory calculations, we found that the difference in the temperature dependence of the peak shift is well understood in terms of the presence/absence of stretching vibration of the intermolecular hydrogen bond in the mode and the change of cell parameters. The anharmonicity in the dissociation potential energy of very weak intermolecular hydrogen bonding causes the remarkable peak shift with temperature in the terahertz spectrum of nicotinamide. This finding suggests that the assignment and identification of peaks in the terahertz spectrum are systematically enabled by temperature-dependent measurements.

Supramolecular structures and assembly and luminescent properties of quinacridone derivatives.

PubMed

Ye, Kaiqi; Wang, Jia; Sun, Hui; Liu, Yu; Mu, Zhongcheng; Li, Fei; Jiang, Shimei; Zhang, Jingying; Zhang, Hongxing; Wang, Yue; Che, Chi-Ming

2005-04-28

The synthesis and single-crystal X-ray structures of two quinacridone derivatives, N,N'-di(n-butyl)quinacridone (1) and N,N'-di(n-butyl)-1,3,8,10-tetramethylquinacridone (2), are reported, and the 1H NMR, absorption, photoluminescent (PL), and electroluminescent (EL) characteristics are presented. Both these crystal structures are characterized by intermolecular pi...pi and hydrogen bonding interactions. The intermolecular pi...pi interactions lead to the formation of molecular columns in the solids of 1 and 2, and the interplanar contact distances between two adjacent molecules are 3.48 and 3.55 angstroms, respectively. Crystals of 1 display shorter intermolecular pi...pi contacts and higher density than 2. These results suggest that tighter intermolecular interactions exist in 1. The 1H NMR, absorption, and PL spectra of 1 and 2 in solutions exhibit concentration-dependent properties. The PL quantum yields of 1 in solutions decrease more quickly with the increase of concentration compared to that of 2 in solutions. For solid thin films of Alq3:1 (Alq3 = tris(8-hydroxyquinolinato)aluminum), emission intensities dramatically decrease and obvious red shifts are observed when the dopant concentration is above 4.2%, while for films of Alq3:2, a similar phenomenon occurs when the concentration is above 6.7%. EL devices with Alq3:1 as emitting layer only show high efficiencies (20.3-14.5 cd/A) within the narrow dopant concentration range of 0.5-1.0%. In contrast, high efficiencies (21.5-12.0 cd/A) are achieved for a wider dopant concentration range of 0.5-5.0% when Alq3:2 films are employed as emitting layer. The different PL and EL concentration-dependent properties of the solid thin films Alq3:1 and Alq3:2 are attributed to their different molecular packing characteristics in the solid state.

Terahertz spectroscopy and solid-state density functional theory calculation of anthracene: Effect of dispersion force on the vibrational modes

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

Zhang, Feng; Tominaga, Keisuke, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp; Hayashi, Michitoshi, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp

2014-05-07

The phonon modes of molecular crystals in the terahertz frequency region often feature delicately coupled inter- and intra-molecular vibrations. Recent advances in density functional theory such as DFT-D{sup *} have enabled accurate frequency calculation. However, the nature of normal modes has not been quantitatively discussed against experimental criteria such as isotope shift (IS) and correlation field splitting (CFS). Here, we report an analytical mode-decoupling method that allows for the decomposition of a normal mode of interest into intermolecular translation, libration, and intramolecular vibrational motions. We show an application of this method using the crystalline anthracene system as an example. Themore » relationship between the experimentally obtained IS and the IS obtained by PBE-D{sup *} simulation indicates that two distinctive regions exist. Region I is associated with a pure intermolecular translation, whereas region II features coupled intramolecular vibrations that are further coupled by a weak intermolecular translation. We find that the PBE-D{sup *} data show excellent agreement with the experimental data in terms of IS and CFS in region II; however, PBE-D{sup *} produces significant deviations in IS in region I where strong coupling between inter- and intra-molecular vibrations contributes to normal modes. The result of this analysis is expected to facilitate future improvement of DFT-D{sup *}.« less

Stress-induced crystal transition of poly(butylene succinate) studied by terahertz and low-frequency Raman spectroscopy and quantum chemical calculation

NASA Astrophysics Data System (ADS)

Tatsuoka, Seika; Sato, Harumi

2018-05-01

We measured terahertz (THz) and low-frequency Raman spectra of Poly (butylene succinate) (PBS) which shows the crystal transition from α to β by stretching. For the assignment of the absorption peaks in the low-frequency region, we performed quantum chemical calculations with Cartesian-coordinate tensor transfer (CCT) method. Four major peaks appeared in the THz spectra of PBS at around 58, 76, 90, and 100 cm-1, and in the low-frequency Raman spectra a peak was observed at 88 cm-1. The THz peak at 100 cm-1 and the Raman peak at 88 cm-1 show a shift to a lower wavenumber region with increasing temperature. The quantum chemical calculation of β crystal form reveals the new peak appears above 100 cm-1. It was found that two kinds of peaks overlapped at around 100 cm-1 in the THz spectra of PBS. One of them can be assigned to a weak hydrogen bond between the C=O and CH2 groups in the intermolecular chains, which is perpendicular to the molecular chain of the α crystal form. Another one showed a parallel polarization which can be assigned to the intramolecular interaction between O (ether) and H-C groups in the β crystal form. The position of the peak at around 100 cm-1 in the perpendicular polarization changed to a lower wavenumber region with stretching, because of the weakening of the intermolecular hydrogen bonding by increasing the interatomic distances. On the other hand, that of the parallel polarization shifts to a higher wavenumber region because of the shortening of the interatomic distance from α to β crystal form (the strength of the intramolecular hydrogen bonding became stronger) by stretching.

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

PubMed

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

2010-09-02

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

The effect of the intermolecular potential formulation on the state-selected energy exchange rate coefficients in N2-N2 collisions.

PubMed

Kurnosov, Alexander; Cacciatore, Mario; Laganà, Antonio; Pirani, Fernando; Bartolomei, Massimiliano; Garcia, Ernesto

2014-04-05

The rate coefficients for N2-N2 collision-induced vibrational energy exchange (important for the enhancement of several modern innovative technologies) have been computed over a wide range of temperature. Potential energy surfaces based on different formulations of the intramolecular and intermolecular components of the interaction have been used to compute quasiclassically and semiclassically some vibrational to vibrational energy transfer rate coefficients. Related outcomes have been rationalized in terms of state-to-state probabilities and cross sections for quasi-resonant transitions and deexcitations from the first excited vibrational level (for which experimental information are available). On this ground, it has been possible to spot critical differences on the vibrational energy exchange mechanisms supported by the different surfaces (mainly by their intermolecular components) in the low collision energy regime, though still effective for temperatures as high as 10,000 K. It was found, in particular, that the most recently proposed intermolecular potential becomes the most effective in promoting vibrational energy exchange near threshold temperatures and has a behavior opposite to the previously proposed one when varying the coupling of vibration with the other degrees of freedom. Copyright © 2014 Wiley Periodicals, Inc.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Multidimensional intermolecular dynamics from tunable far-infrared laser spectroscopy: Angular-radial coupling in the intermolecular potential of argon--H sub 2 O

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

Cohen, R.C.; Saykally, R.J.

1991-12-01

Five new vibration--rotation tunneling states of Ar--H{sub 2}O (the {Sigma} and {Pi}(1{sub 11}) and the {Sigma} and {Pi}(2{sub 12}) internal rotor states and the {ital n}=1, {Pi}(1{sub 01}) stretching-internal rotor combination level) have been accessed by tunable far-infrared laser spectroscopy. The measured vibrational band origins of transitions to these states are within 2% of predictions made from an anisotropic three-dimensional intermolecular potential surface (denoted AW1) derived from a nonlinear least-squares fit to previous far-infrared spectral data (J. Phys. Chem. {bold 94}, 7991(1990)). This provides strong evidence that the AW1 intermolecular potential surface incorporates much of the essential physics of themore » intermolecular forces which bind the cluster. However, larger deviations from the predictions are found in the observed rotational term values. A detailed analysis of these deviations clearly demonstrates the need for even stronger angular-radial coupling in the Ar--H{sub 2}O intermolecular potential than the already substantial coupling present in the AW1 surface. Specifically, the presently observed {Sigma}(1{sub 11}) state and the {ital n}=1, {Sigma}(0{sub 00}) state are found to be approximately 65:35 mixtures of the basis states which represent pure stretching and internal rotation. The {Sigma}(2{sub 12}) level is found to be mixed just as strongly with {ital n}=2, {Sigma}(1{sub 01}). The formalism for accurately deperturbing vibration--rotation--tunneling states coupled by Coriolis interactions used in the above analysis is presented.« less

Are Noncovalent Interactions an Achilles Heel in Chemistry Education? A Comparison of Instructional Approaches

ERIC Educational Resources Information Center

Williams, Leah C.; Underwood, Sonia M.; Klymkowsky, Michael W.; Cooper, Melanie M.

2015-01-01

Intermolecular forces (IMFs), or more broadly, noncovalent interactions either within or between molecules, are central to an understanding of a wide range of chemical and biological phenomena. In this study, we present a multiyear, multi-institutional, longitudinal comparison of how students enrolled in traditional general chemistry courses and…

Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

PubMed Central

Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

2014-01-01

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor. PMID:25001596

Infrared Spectroscopy of Hydrogen in Fullerite and MOF-5 Hosts

NASA Astrophysics Data System (ADS)

Fitzgerald, Stephen; Churchill, Hugh; Korngut, Phil; Simmons, Christie; Strangas, Yorgos

2006-03-01

We present a novel use of diffuse reflectance infrared spectroscopy to study the quantum dynamics of hydrogen molecules trapped within a host material. This technique is particularly useful for the study of hydrogen storage materials since it provides detailed information about the intermolecular potential at the binding site. Because H2 has no intrinsic infrared activity any observed features arise solely through interaction with the host material and as such are very sensitive to the symmetry of the binding site. The drawback is that the induced spectra are quite weak. However, a technique based on diffuse reflectance has been shown to produce a sufficiently large signal [1]. We have now constructed a cryogenic system that allows spectra to be obtained in this manner at pressures as high as 100 atm. and at temperatures as low as 10 K. Data will be presented for H2 in both C60 and MOF-5 showing a series of absorption features arising from the quantized vibrational, rotational, and translational motion of the trapped H2. At the lowest temperature these peaks become quite sharp, FWHM less than 1 cm-1, with a detailed fine structure arising from the H2 host interactions. 1. S. A. FitzGerald et al., Phys. Rev. B 65, 140302. (2002)

Crystal structure, vibrational and theoretical studies of bis(4-amino-1,2,4-triazolium) hexachloridostannate(IV)

NASA Astrophysics Data System (ADS)

Daszkiewicz, Marek; Marchewka, Mariusz K.

2012-06-01

X-ray structure of new hybrid organic-inorganic compound, bis(4-amino-1,2,4-triazolium) hexachloridostannate(IV), [1t(4at)]2SnCl6 (P1¯ space group) was determined. Crystal structure of 4-amino-1,2,4-triazole (Pbca space group) was reinvestigated. Non-planar orientation of NH2 group was found. The geometry of the amino group does not significantly change upon protonation. The route of protonation of 4-aminotriazole and tautomer equilibrium constants for the cationic forms were theoretically studied by means of B3LYP/6-31G* method. The most stable monoprotonated species is 1H-trans-4-amino-1,2,4-triazole, 1t(4at)+, whereas the final product of the protonation route is 12(4at)2+. Potential Energy Distribution (PED) analysis was carried out for two conformers, 1c(4at)+ and 1t(4at)+. Very good agreement between theoretical and experimental frequencies was achieved due to very weak interactions existing in [1t(4at)]2SnCl6. Infrared and Raman bands were assigned on the basis of PED analysis. Comparison of vibrational spectra of [1t(4at)]2SnCl6 and [1t(4at)]Cl indicates significantly weaker intermolecular interactions in the former compound.

Protein substitution affects glass transition temperature and thermal stability.

PubMed

Budhavaram, Naresh K; Miller, Jonathan A; Shen, Ying; Barone, Justin R

2010-09-08

When proteins are removed from their native state they suffer from two deficiencies: (1) glassy behavior with glass transition temperatures (Tg) well above room temperature and (2) thermal instability. The glassy behavior originates in multiple hydrogen bonds between amino acids on adjacent protein molecules. Proteins, like most biopolymers, are thermally unstable. Substituting ovalbumin with linear and cyclic substituents using a facile nucleophilic addition reaction can affect Tg and thermal stability. More hydrophobic linear substituents lowered Tg by interrupting intermolecular interactions and increasing free volume. More hydrophilic and cyclic substituents increased thermal stability by increasing intermolecular interactions. In some cases, substituents instituted cross-linking between protein chains that enhanced thermal stability. Internal plasticization using covalent substitution and external plasticization using low molecular weight polar liquids show the same protein structural changes and a signature of plasticization is identified.

Crowding Effects on the Formation and Maintenance of Nuclear Bodies: Insights from Molecular-Dynamics Simulations of Simple Spherical Model Particles

PubMed Central

Cho, Eun Jin; Kim, Jun Soo

2012-01-01

The physics of structure formation and maintenance of nuclear bodies (NBs), such as nucleoli, Cajal bodies, promyelocytic leukemia bodies, and speckles, in a crowded nuclear environment remains largely unknown. We investigate the role of macromolecular crowding in the formation and maintenance of NBs using computer simulations of a simple spherical model, called Lennard-Jones (LJ) particles. LJ particles form a one-phase, dilute fluid when the intermolecular interaction is weaker than a critical value, above which they phase separate and form a condensed domain. We find that when volume-exclusive crowders exist in significant concentrations, domain formation is induced even for weaker intermolecular interactions, and the effect is more pronounced with increasing crowder concentration. Simulation results show that a previous experimental finding that promyelocytic leukemia bodies disappear in the less-crowded condition and reassemble in the normal crowded condition can be interpreted as a consequence of the increased intermolecular interactions between NB proteins due to crowding. Based on further analysis of the simulation results, we discuss the acceleration of macromolecular associations that occur within NBs, and the delay of diffusive transport of macromolecules within and out of NBs when the crowder concentration increases. This study suggests that in a polydisperse nuclear environment that is enriched with a variety of macromolecules, macromolecular crowding not only plays an important role in the formation and maintenance of NBs, but also may perform some regulatory functions in response to alterations in the crowding conditions. PMID:22947858

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

PubMed

Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

2017-02-15

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala) n n ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala) 2 , as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

Intermolecular interaction studies of glyphosate with water

NASA Astrophysics Data System (ADS)

Manon, Priti; Juglan, K. C.; Kaur, Kirandeep; Sethi, Nidhi; Kaur, J. P.

2017-07-01

The density (ρ), viscosity (η) and ultrasonic velocity (U) of glyphosate with water have been measured on different ultrasonic frequency ranges from 1MHz, 2MHz, 3MHz & 5MHz by varying concentrations (0.05%, 0.10%, 0.15%, 0.20%, 0.25%, 0.30%, 0.35%, & 0.40%) at 30°C. The specific gravity bottle, Ostwald's viscometer and quartz crystal interferometer were used to determine density (ρ), viscosity (η) and ultrasonic velocity (U). These three factors contribute in evaluating the other parameters as acoustic impedance (Z), adiabatic compressibility (β), relaxation time (τ), intermolecular free length (Lf), free volume (Vf), ultrasonic attenuation (α/f2), Rao's constant (R), Wada's constant (W) and relative strength (R). Solute-solvent interaction is confirmed by ultrasonic velocity and viscosity values, which increases with increase in concentration indicates stronger association between solute and solvent molecules. With rise in ultrasonic frequency the interaction between the solute and solvent particles decreases. The linear variations in Rao's constant and Wada's constant suggest the absence of complex formation.

Enthalpy characteristics of L-proline dissolution in certain water-organic mixtures at 298.15 K

NASA Astrophysics Data System (ADS)

Badelin, V. G.; Smirnov, V. I.

2017-01-01

A thermochemical study of the processes of L-proline dissolution in aqueous solutions of acetonitrile, 1,4-dioxane, acetone, dimethyl sulfoxide, nitromethane and tetrahydrofuran at T = 298.15 K in the range of organic solvent concentrations x2 = 0-0.25 mole fractions is performed. Standard values of the enthalpies of solution and transfer of L-proline from water to mixed solvent, and the enthalpy coefficients of pairwise interactions between L-proline and molecules of organic solvents, are calculated. The effect the composition of a water-organic mixture and the structure of organic solvents have on the enthalpy characteristics of L-proline dissolution and transfer is examined. The effect the energy properties of intermolecular interactions between components of a mixed solvent has on the intermolecular interactions between L-proline and molecules of cosolvent is estimated. The correlation between the enthalpy characteristics of L-proline dissolution and electron-donor properties of organic cosolvent in aqueous solutions is determined.

The effect of cesium carbonate on 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C{sub 61} aggregation in films

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

Lindemann, William R.; Wang, Wenjie; Shinar, Joseph

2014-11-10

Surface-pressure versus molecular area isotherms, X-ray reflectivity, and X-ray near-total reflection fluorescence were used to study the properties of 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C{sub 61} (PCBM) that was pre-mixed with cesium carbonate and spread as a film at the air-water interface. The pre-mixed PCBM with cesium carbonate demonstrated a strikingly strong effect on the organization of the film. Whereas films formed from pure PCBM solution were rough due to strong inter-molecular interactions, the films formed from the mixture were much smoother. This indicates that the cesium carbonate moderates the inter-molecular interactions among PCBM molecules, hinting that the cesium diffusion observed in inverted organic photovoltaicmore » structures and the likely ensuing ionic Cs-PCBM interaction decrease aggregation tendency of PCBM. This implies that the use of cesium salts affects the morphology of the organic layer and consequently improves the efficiency of these devices.« less

The effect of cesium carbonate on 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C 61 aggregation in films

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

Lindemann, William R.; Wang, Wenjie; Fungura, Fadzai

2014-11-11

Surface-pressure isotherms, X-ray reflectivity, and X-ray near-total reflection fluorescence were used to study the properties of 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C 61 (PCBM) that was pre-mixed with cesium carbonate and spread as a film at the air-water interface. The pre-mixed PCBM with cesium carbonate demonstrated a strikingly strong effect on the organization of the film. Whereas films formed from pure PCBM solution were rough due to strong inter-molecular interactions, the films formed from the mixture were much smoother. This indicates that the cesium carbonate moderates the inter-molecular interactions among PCBM molecules, hinting that the cesium diffusion observed in inverted organic photovoltaics and the likelymore » ensuing ionic Cs-PCBM interaction decrease aggregation tendency of PCBM. As a result, this implies that the use of cesium salts affects the morphology of the organic layer and consequently improves the efficiency of these devices.« less

Hydrogen and dihydrogen bonding of transition metal hydrides

NASA Astrophysics Data System (ADS)

Jacobsen, Heiko

2008-04-01

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

Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides.

PubMed

Yu, Hua; Wang, Mao-jun; Xuan, Nan-xia; Shang, Zhi-cai; Wu, Jun

2015-10-01

To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding. van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues.

Determination and Quantification of Molecular Interactions in Protein Films: A Review.

PubMed

Hammann, Felicia; Schmid, Markus

2014-12-10

Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography) and analysis of solid films (spectroscopy techniques, X-ray scattering methods). To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

Determination Quantification of Molecular Interactions in Protein Films: A Review

PubMed Central

Hammann, Felicia; Schmid, Markus

2014-01-01

Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography) and analysis of solid films (spectroscopy techniques, X-ray scattering methods). To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins. PMID:28788285

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen.

PubMed

Andersen, J; Voute, A; Mihrin, D; Heimdal, J; Berg, R W; Torsson, M; Wugt Larsen, R

2017-06-28

The true global potential energy minimum configuration of the formaldehyde dimer (CH 2 O) 2 , including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of C s and C 2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar C s configuration of (CH 2 O) 2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol -1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol -1 for the dissociation energy D 0 of this global potential energy minimum.

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen

NASA Astrophysics Data System (ADS)

Andersen, J.; Voute, A.; Mihrin, D.; Heimdal, J.; Berg, R. W.; Torsson, M.; Wugt Larsen, R.

2017-06-01

The true global potential energy minimum configuration of the formaldehyde dimer (CH2O)2, including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of Cs and C2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar Cs configuration of (CH2O)2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol-1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol-1 for the dissociation energy D0 of this global potential energy minimum.

Molecular dynamics study of polysaccharides in binary solvent mixtures of an ionic liquid and water.

PubMed

Liu, Hanbin; Sale, Kenneth L; Simmons, Blake A; Singh, Seema

2011-09-01

Some ionic liquids (ILs) have great promise as effective solvents for biomass pretreatment, and there are several that have been reported that can dissolve large amounts of cellulose. The solubilized cellulose can then be recovered by addition of antisolvents, such as water or ethanol, and this regeneration process plays an important role in the subsequent enzymatic saccharification reactions and in the recovery of the ionic liquid. To date, little is known about the fundamental intermolecular interactions that drive the dissolution and subsequent regeneration of cellulose in complex mixtures of ionic liquids, water, and cellulose. To investigate these interactions, in this work, molecular dynamics (MD) simulations were carried out to study binary and ternary mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) with water and a cellulose oligomer. Simulations of a cellulose oligomer dissolved in three concentrations of binary mixtures of [C2mim][OAc] and water were used to represent the ternary system in the dissolution phase (high [C2mim][OAc] concentration) and present during the initial phase of the regeneration step (intermediate and low [C2mim][OAc] concentrations). The MD analysis of the structure and dynamics that exist in these binary and ternary mixtures provides information on the key intermolecular interactions between cellulose and [C2mim][OAc] that lead to dissolution of cellulose and the key intermolecular interactions in the intermediate states of cellulose precipitation as a function of water content in the cellulose/IL/water system. The analysis of this intermediate state provides new insight into the molecular driving forces present in this ternary system. © 2011 American Chemical Society

The impact of the Fermi-Dirac distribution on charge injection at metal/organic interfaces.

PubMed

Wang, Z B; Helander, M G; Greiner, M T; Lu, Z H

2010-05-07

The Fermi level has historically been assumed to be the only energy-level from which carriers are injected at metal/semiconductor interfaces. In traditional semiconductor device physics, this approximation is reasonable as the thermal distribution of delocalized states in the semiconductor tends to dominate device characteristics. However, in the case of organic semiconductors the weak intermolecular interactions results in highly localized electronic states, such that the thermal distribution of carriers in the metal may also influence device characteristics. In this work we demonstrate that the Fermi-Dirac distribution of carriers in the metal has a much more significant impact on charge injection at metal/organic interfaces than has previously been assumed. An injection model which includes the effect of the Fermi-Dirac electron distribution was proposed. This model has been tested against experimental data and was found to provide a better physical description of charge injection. This finding indicates that the thermal distribution of electronic states in the metal should, in general, be considered in the study of metal/organic interfaces.

One pot synthesis of two Mn(II) perchlorate complexes with s-triazine NNN-pincer ligand; molecular structure, Hirshfeld analysis and DFT studies

NASA Astrophysics Data System (ADS)

Soliman, Saied M.; El-Faham, Ayman

2018-07-01

Self assembly of Mn(II) perchlorate and bis(pyrazolo)-s-triazine pincer ligand (L) in methanol-water mixture afforded the homoleptic [MnL2](ClO4)2 complex (1) as plate colorless crystals. Following the crystallization process till the near dryness of the solution, we noted few needle like crystals of the heteroleptic [MnL(H2O)3](ClO4)2·H2O complex (2). Their molecular and supramolecular structures were analyzed using single crystal structure combined with Hirshfeld analysis. The packing of complexes 1 and 2 is dominated by weak Csbnd H⋯O and strong Osbnd H⋯O hydrogen bonds, respectively, as well as anion-π stacking interactions. Using Hirshfeld analysis, the percentages of the O⋯H intermolecular contacts are 32.7% and 36.8% for 1 and 2, respectively. The Mnsbnd N distances correlated well with the atoms in molecules (AIM) topological parameters. The amount of electron density transferred from the ligand units to the manganese centre are nearly the same (0.9 e) in both complexes.

Concise NMR approach for molecular dynamics characterizations in organic solids.

PubMed

Aliev, Abil E; Courtier-Murias, Denis

2013-08-22

Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics.

Differentiations of Enantiomers via Their Diasteriomeric Association Complexes--There Are Two Ways of Shaking Hands

ERIC Educational Resources Information Center

Mannschreck, Albrecht; Kiesswetter, Roland

2005-01-01

The intermolecular interaction of one enantiomer with a chiral auxiliary molecule may differ from the interaction of the other enantiomer with the same auxiliary molecule, explained by the example of unequal handshakes. This methodology helps present a lecture to the students that emphasizes the basic similarity of the association-based…

Helping Students Assess the Relative Importance of Different Intermolecular Interactions

ERIC Educational Resources Information Center

Jasien, Paul G.

2008-01-01

A semi-quantitative model has been developed to estimate the relative effects of dispersion, dipole-dipole interactions, and H-bonding on the normal boiling points ("T[subscript b]") for a subset of simple organic systems. The model is based upon a statistical analysis using multiple linear regression on a series of straight-chain organic…

Amorphous stabilization and dissolution enhancement of amorphous ternary solid dispersions: combination of polymers showing drug-polymer interaction for synergistic effects.

PubMed

Prasad, Dev; Chauhan, Harsh; Atef, Eman

2014-11-01

The purpose of this study was to understand the combined effect of two polymers showing drug-polymer interactions on amorphous stabilization and dissolution enhancement of indomethacin (IND) in amorphous ternary solid dispersions. The mechanism responsible for the enhanced stability and dissolution of IND in amorphous ternary systems was studied by exploring the miscibility and intermolecular interactions between IND and polymers through thermal and spectroscopic analysis. Eudragit E100 and PVP K90 at low concentrations (2.5%-40%, w/w) were used to prepare amorphous binary and ternary solid dispersions by solvent evaporation. Stability results showed that amorphous ternary solid dispersions have better stability compared with amorphous binary solid dispersions. The dissolution of IND from the ternary dispersion was substantially higher than the binary dispersions as well as amorphous drug. Melting point depression of physical mixtures reveals that the drug was miscible in both the polymers; however, greater miscibility was observed in ternary physical mixtures. The IR analysis confirmed intermolecular interactions between IND and individual polymers. These interactions were found to be intact in ternary systems. These results suggest that the combination of two polymers showing drug-polymer interaction offers synergistic enhancement in amorphous stability and dissolution in ternary solid dispersions. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

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

PubMed

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

2016-07-01

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

Origin of Enantioselectivity in CF3-PIP-Catalyzed Kinetic Resolution of Secondary Benzylic Alcohols

PubMed Central

Li, Ximin; Liu, Peng; Houk, K. N.; Birman, Vladimir B.

2009-01-01

Computational studies provide support for the involvement of intermolecular π–interactions in the chiral recognition of secondary benzylic alcohols by the enantioselective acyl transfer catalyst CF3-PIP. PMID:18817392

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

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Infrared and Ultraviolet Spectroscopy of Gas-Phase Imidazolium and Pyridinium Ionic Liquids.

NASA Astrophysics Data System (ADS)

Young, Justin W.; Booth, Ryan S.; Annesley, Christopher; Stearns, Jaime A.

2015-06-01

Ionic liquids (ILs) are a highly variable and potentially game-changing class of molecules for a number of Air Force applications such as satellite propulsion, but the complex nature of IL structure and intermolecular interactions makes it difficult to adequately predict structure-property relationships in order to make new IL-based technology a reality. For example, methylation of imidazolium ionic liquids leads to a substantial increase in viscosity but the underlying physical mechanism is not understood. In addition, the role of hydrogen bonding in ILs, and especially its relationship to macroscopic properties, is a matter of ongoing research. Here we describe the gas-phase spectroscopy of a series of imidazolium- and pyridinium-based ILs, using a combination of infrared spectroscopy and density functional theory to establish the intermolecular interactions present in various ILs, to assess how well they are described by theory, and to relate microscopic structure to macroscopic properties.

Synthesis, characterization, AIM and NBO analysis of HMX/DMI cocrystal explosive

NASA Astrophysics Data System (ADS)

Lin, He; Zhu, Shun-Guan; Li, Hong-Zhen; Peng, Xin-Hua

2013-09-01

1,3,5,7-Tetranitro-1,3,5,7-tetrazacyclooctane (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal explosive was synthesized and characterized by using X-ray single crystal diffraction. HMX/DMI cocrystal crystallizes in the monoclinic system (space group Cm), with cell parameters a = 7.231(2)Å, b = 14.739(2)Å, c = 7.552(1)Å, β = 96.66°. In addition, density functional theory, involving binding energy, natural bond orbital (NBO) analysis, atoms in molecule (AIM) analysis, band structure, and density of states, was adopted to investigate intermolecular interactions for the formation of HMX/DMI cocrystal. The results show that hydrogen bondings between methylene groups of HMX molecules and O atoms of DMI molecules are the main intermolecular interactions. This research provides the basis for further design of cocrystal explosives, which are composed of HMX and energetic materials.

Crystal structure, spectrum character and explosive property of a new cocrystal CL-20/DNT

NASA Astrophysics Data System (ADS)

Liu, Ke; Zhang, Gao; Luan, Jieyu; Chen, Zhiqun; Su, Pengfei; Shu, Yuanjie

2016-04-01

A new cocrystal explosive of 2,4,6,8,10,12-hexanitrohexaazaiso-wurtzitane(CL-20) and 2,5-dinitrotoluene(DNT) in a molar ratio of 1:2 has been prepared by slow solvent evaporation method. Crystal structure of the cocrystal characterized by single crystal X-ray diffraction (SXRD) reveals that the cocrystal is formed by intermolecular hydrogen bond interactions and belongs to the triclinic system with P-1 group. Moreover, the obivious differences of powder X-ray diffraction (PXRD) patterns, infrared spectroscopy and Raman spectroscopy confirm that the intermolecular interactions have great influence for the crystal structure and formation of cocrystal. The cocrystal exhibits a lower impact height of 44 cm, suggesting a substantial reduction of sensitivity in comparison with CL-20. And thermal test results showed cocrystal obtains a lower melting point than DNT, which means huge advantages in blasting engineering.

Lattice dynamical and dielectric properties of L-amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2006-08-01

We present the results of ab initio calculations of the lattice dynamical and dielectric properties of the L-amino acids L-alanine, L-leucine, and L-isoleucine. Normal-mode frequencies and dielectric permittivity tensors are obtained using density-functional perturbation theory implemented within the plane-wave pseudopotential approximation. IR spectra are calculated and are used to analyze the effects of intermolecular interactions and zwitterionization upon the lattice dynamics. It is found that vibronic modes associated with the carboxy and amino functional groups undergo modification from their free-molecule values due to the presence of hydrogen bonds. The role of macroscopic electric fields set up by zone-center normal modes in the lattice dynamics is investigated by analysis of the Born effective charge. Calculated permittivity tensors are found to be greater than would be obtained by a naive use of the isolated molecular values, indicating the role of intermolecular interactions in increasing molecular polarizability.

Comparative structural analysis of cytidine, ethenocytidine and their protonated salts III. 1H, 13C and 15N NMR studies at natural isotope abundance.

PubMed Central

Kozerski, L; Sierzputowska-Gracz, H; Krzyzosiak, W; Bratek-Wiewiórowska, M; Jaskólski, M; Wiewiórowski, M

1984-01-01

The 1H, 13C, 15N NMR spectra of cytidine /Cyd/, ethenocytidine /epsilon Cyd/ and their hydrochlorides /Cyd X HC1/ and /epsilon Cyd X HC1/ have been analysed to compare structural differences observed in solution with those existing in the crystalline state. The effects of ethenobridging and protonation of the hertero-aromatic base on the intramolecular stereochemistry, intermolecular interactions and electronic structure of the whole molecule are discussed on the basis of the NMR studies in DMSO solutions. Particular interest is devoted to the discussion of the conformation of the ribose ring, the presence of the intramolecular C-5'-0...H-6-C hydrogen bond, unambiguous assignment of the site of protonation, the mechanism of the 5C-H deuterium exchange in Cyd X HC1, and the intermolecular interactions in solution. PMID:6701098

Chromatographic and spectroscopic methods for the determination of solvent properties of room temperature ionic liquids.

PubMed

Poole, Colin F

2004-05-28

Room temperature ionic liquids are novel solvents with favorable environmental and technical features. Synthetic routes to over 200 room temperature ionic liquids are known but for most ionic liquids physicochemical data are generally lacking or incomplete. Chromatographic and spectroscopic methods afford suitable tools for the study of solvation properties under conditions that approximate infinite dilution. Gas-liquid chromatography is suitable for the determination of gas-liquid partition coefficients and activity coefficients as well as thermodynamic constants derived from either of these parameters and their variation with temperature. The solvation parameter model can be used to define the contribution from individual intermolecular interactions to the gas-liquid partition coefficient. Application of chemometric procedures to a large database of system constants for ionic liquids indicates their unique solvent properties: low cohesion for ionic liquids with weakly associated ions compared with non-ionic liquids of similar polarity; greater hydrogen-bond basicity than typical polar non-ionic solvents; and a range of dipolarity/polarizability that encompasses the same range as occupied by the most polar non-ionic liquids. These properties can be crudely related to ion structures but further work is required to develop a comprehensive approach for the design of ionic liquids for specific applications. Data for liquid-liquid partition coefficients is scarce by comparison with gas-liquid partition coefficients. Preliminary studies indicate the possibility of using the solvation parameter model for interpretation of liquid-liquid partition coefficients determined by shake-flask procedures as well as the feasibility of using liquid-liquid chromatography for the convenient and rapid determination of liquid-liquid partition coefficients. Spectroscopic measurements of solvatochromic and fluorescent probe molecules in room temperature ionic liquids provide insights into solvent intermolecular interactions although interpretation of the different and generally uncorrelated "polarity" scales is sometimes ambiguous. All evidence points to the ionic liquids as a unique class of polar solvents suitable for technical development. In terms of designer solvents, however, further work is needed to fill the gaps in our knowledge of the relationship between ion structures and physicochemical properties.

Structural phase transition of magnetic [Ni(dmit)2]- salts induced by supramolecular cation structures of (M+)([12]crown-4)2.

PubMed

Akutagawa, Tomoyuki; Motokizawa, Takeshi; Matsuura, Kazumasa; Nishihara, Sadafumi; Noro, Shin-ichiro; Nakamura, Takayoshi

2006-03-30

Sandwich-type supramolecular cation structures of (M(+))([12]crown-4)(2) complexes (M(+) = Li(+), Na(+), K(+), and Rb(+)) were introduced as countercations to the [Ni(dmit)(2)](-) anion, which bears an S = (1)/(2) spin, to form novel magnetic crystals (dmit(2-) = 2-thione-1,3-dithiole-4,5-dithiolate). The zigzag arrangement of Li(+)([12]crown-4)(2) cations in Li(+)([12]crown-4)(2)[Ni(dmit)(2)](-) salt induced weak intermolecular interactions of [Ni(dmit)(2)](-) dimers, whose magnetic spins were isolated from each other. The molecular arrangements of cations and anions in M(+)([12]crown-4)(2)[Ni(dmit)(2)](-) salts (M(+) = Na(+), K(+), and Rb(+)) were isostructural to each other. In the case of Na(+)([12]crown-4)(2)[Ni(dmit)(2)](-), the space group C2/m changed to C2/c with a lowering in temperature from 298 to 100 K. This structural change occurred at 222.5 K as a first-order phase transition. The space group C2/m (T = 298 K) in the salt K(+)([12]crown-4)(2)[Ni(dmit)(2)](-) also changed to C2/c (T = 100 K), which transition occurred at 270 K. Crystal structural analyses at 298 and 100 K revealed changes in both supramolecular cation conformation and [Ni(dmit)(2)](-) anion arrangements. The transition from C2/m to C2/c crystals generated a dipole moment in the Na(+)([12]crown-4)(2) and K(+)([12]crown-4)(2) structures, which were reconstructed to cancel the net dipole moment of the C2/c crystals. These cation transformations led to changes in intermolecular interactions between the [Ni(dmit)(2)](-) anions via structural rearrangements. The crystal structure of C2/c was stabilized in Rb(+)([12]crown-4)(2)[Ni(dmit)(2)](-) at 298 K. The [Ni(dmit)(2)](-) configuration in these salts with the C2/c space group was a one-dimensional uniform chain, which showed the temperature-dependent magnetic susceptibility of a one-dimensional linear Heisenberg antiferromagnetic chain.

First-principles binary diffusion coefficients for H, H 2 and four normal alkanes + N 2

DOE PAGES

Jasper, Ahren W.; Kamarchik, Eugene; Miller, James A.; ...

2014-09-30

Collision integrals related to binary (dilute gas) diffusion are calculated classically for six species colliding with N 2. The most detailed calculations make no assumptions regarding the complexity of the potential energy surface, and the resulting classical collision integrals are in excellent agreement with previous semiclassical results for H + N 2 and H 2 + N 2 and with recent experimental results for C n H 2n+2 + N 2, n = 2–4. The detailed classical results are used to test the accuracy of three simplifying assumptions typically made when calculating collision integrals: (1) approximating the intermolecular potential asmore » isotropic, (2) neglecting the internal structure of the colliders (i.e., neglecting inelasticity), and (3) employing unphysical R –12 repulsive interactions. The effect of anisotropy is found to be negligible for H + N 2 and H 2 + N 2 (in agreement with previous quantum mechanical and semiclassical results for systems involving atomic and diatomic species) but is more significant for larger species at low temperatures. For example, the neglect of anisotropy decreases the diffusion coefficient for butane + N 2 by 15% at 300 K. The neglect of inelasticity, in contrast, introduces only very small errors. Approximating the repulsive wall as an unphysical R –12 interaction is a significant source of error at all temperatures for the weakly interacting systems H + N 2 and H 2 + N 2, with errors as large as 40%. For the normal alkanes in N 2, which feature stronger interactions, the 12/6 Lennard–Jones approximation is found to be accurate, particularly at temperatures above –700 K where it predicts the full-dimensional result to within 5% (although with somewhat different temperature dependence). Overall, the typical practical approach of assuming isotropic 12/6 Lennard–Jones interactions is confirmed to be suitable for combustion applications except for weakly interacting systems, such as H + N 2. For these systems, anisotropy and inelasticity can safely be neglected but a more detailed description of the repulsive wall is required for quantitative predictions. Moreover, a straightforward approach for calculating effective isotropic potentials with realistic repulsive walls is described. An analytic expression for the calculated diffusion coefficient for H + N 2 is presented and is estimated to have a 2-sigma error bar of only 0.7%.« less

N-(Quinolin-8-yl)quinoline-2-carbox­amide

PubMed Central

Li, Yanfeng; Zhou, Hongbo; Shen, Xiaoping

2012-01-01

In the title compound, C19H13N3O, the dihedral angle between the two quinoline systems is 11.54 (3)°. The mol­ecular conformation is stabilized by intra­molecular N—H⋯N and C—H⋯O hydrogen bonds, with N—H⋯N being bifurcated towards the two N atoms of the two quinoline rings. In the crystal, there are weak intermolecular π–π inter­actions present involving the quinoline rings [centroid–centroid distance 3.7351 (14) Å]. PMID:22719482

Trisphenalenyl-based neutral radical molecular conductor.

PubMed

Pal, Sushanta K; Itkis, Mikhail E; Tham, Fook S; Reed, Robert W; Oakley, Richard T; Haddon, Robert C

2008-03-26

We report the preparation, crystallization, and solid-state characterization of the first member of a new family of tris(1,9-disubstituted phenalenyl)silicon neutral radicals. In the solid state, the radical packs as weak partial pi-dimers with intermolecular carbon...carbon contacts that fall at the van der Waals atomic separation. Magnetic susceptibility measurements indicate approximately 0.7 Curie spins per molecule from room temperature down to 50 K, below which antiferromagnetic coupling becomes apparent; the compound has a room-temperature single-crystal conductivity of sigmaRT = 2.4 x 10(-6) S cm(-1).

Methanol clusters (CH3OH)n: putative global minimum-energy structures from model potentials and dispersion-corrected density functional theory.

PubMed

Kazachenko, Sergey; Bulusu, Satya; Thakkar, Ajit J

2013-06-14

Putative global minima are reported for methanol clusters (CH3OH)n with n ≤ 15. The predictions are based on global optimization of three intermolecular potential energy models followed by local optimization and single-point energy calculations using two variants of dispersion-corrected density functional theory. Recurring structural motifs include folded and/or twisted rings, folded rings with a short branch, and stacked rings. Many of the larger structures are stabilized by weak C-H···O bonds.

Theoretical Models for Surface Forces and Adhesion and Their Measurement Using Atomic Force Microscopy

PubMed Central

Leite, Fabio L.; Bueno, Carolina C.; Da Róz, Alessandra L.; Ziemath, Ervino C.; Oliveira, Osvaldo N.

2012-01-01

The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of AFS, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution. PMID:23202925

Nitroxide stable radicals interacting as Lewis bases in hydrogen bonds: A search in the Cambridge structural data base for intermolecular contacts

NASA Astrophysics Data System (ADS)

Alkorta, Ibon; Elguero, José; Elguero, Eric

2017-11-01

1125 X-ray structures of nitroxide free radicals presenting intermolecular hydrogen bonds have been reported in the Cambridge Structural Database. We will report in this paper a qualitative and quantitative analysis of these bonds. The observation in some plots of an excluded region was statistically analyzed using convex hull and kernel smooting methodologies. A theoretical study at the MP2 level with different basis has been carried out indicating that the nitronyl nitroxide radicals (five electrons) lie just in between nitroso compounds (four electrons) and amine N-oxides (six electrons) as far as hydrogen-bond basicity is concerned.

Quantum mechanical study of pre-dissociation enhancement of linear and nonlinear polarizabilities of (TeO2)(n) oligomers as a key to understanding the remarkable dielectric properties of TeO2 glasses.

PubMed

Smirnov, Mikhail; Mirgorodsky, Andrei; Masson, Olivier; Thomas, Philippe

2012-09-20

The effects of intermolecular interactions of TeO(2) molecules in the (TeO(2))(n) oligomers on the polarizability (α) and second hyperpolarizability (γ) are investigated by the use of a density functional method. A significant intermolecular distance dependence of both quantities is observed. The huge dissociation-induced polarizability enhancement is analyzed in terms of the molecular orbital evolution. It is shown that the obtained results can provide a new look at the microscopic origin of the extraordinary dielectric properties of TeO(2) glass.

The synthesis and structures of 1,1'-bis(sulfonyl)ferrocene derivatives.

PubMed

Chanawanno, Kullapa; Holstrom, Cole; Crandall, Laura A; Dodge, Henry; Nemykin, Victor N; Herrick, Richard S; Ziegler, Christopher J

2016-09-28

A series of 1,1'-bis(sulfonyl)ferrocene compounds were produced via the 1,1'-bis(sulfonate)ferrocene ammonium salt. This compound can be readily converted to 1,1' bis(sulfonylchloride)ferrocene. By varying stoichiometry and reaction times, both mono- and bis-sulfonamide derivatives can be synthesized. All new compounds presented in this report have been structurally characterized. The structures of the bis-sulfonamide systems are similar to the well-studied bis(amide) ferrocene compounds. Intermolecular hydrogen bonding is observed, typically between NH and SO groups of neighboring sulfonamides. However in the bis(GABA) derivative, intermolecular NH to CO hydrogen bonding interactions are present.

Small Molecule Activation by Intermolecular Zr(IV)-Phosphine Frustrated Lewis Pairs.

PubMed

Metters, Owen J; Forrest, Sebastian J K; Sparkes, Hazel A; Manners, Ian; Wass, Duncan F

2016-02-17

We report intermolecular transition metal frustrated Lewis pairs (FLPs) based on zirconocene aryloxide and phosphine moieties that exhibit a broad range of small molecule activation chemistry that has previously been the preserve of only intramolecular pairs. Reactions with D2, CO2, THF, and PhCCH are reported. By contrast with previous intramolecular examples, these systems allow facile access to a variety of steric and electronic characteristics at the Lewis acidic and Lewis basic components, with the three-step syntheses of 10 new intermolecular transition metal FLPs being reported. Systematic variation to the phosphine Lewis base is used to unravel steric considerations, with the surprising conclusion that phosphines with relatively small Tolman steric parameters not only give highly reactive FLPs but are often seen to have the highest selectivity for the desired product. DOSY NMR spectroscopic studies on these systems reveal for the first time the nature of the Lewis acid/Lewis base interactions in transition metal FLPs of this type.

Multiple-decker phthalocyaninato dinuclear lanthanoid(III) single-molecule magnets with dual-magnetic relaxation processes.

PubMed

Katoh, Keiichi; Horii, Yoji; Yasuda, Nobuhiro; Wernsdorfer, Wolfgang; Toriumi, Koshiro; Breedlove, Brian K; Yamashita, Masahiro

2012-11-28

The SMM behaviour of dinuclear Ln(III)-Pc multiple-decker complexes (Ln = Tb(3+) and Dy(3+)) with energy barriers and slow-relaxation behaviour were explained by using X-ray crystallography and static and dynamic susceptibility measurements. In particular, interactions among the 4f electrons of several dinuclear Ln(III)-Pc type SMMs have never been discussed on the basis of the crystal structure. For dinuclear Tb(III)-Pc complexes, a dual magnetic relaxation process was observed. The relaxation processes are due to the anisotropic centres. Our results clearly show that the two Tb(3+) ion sites are equivalent and are consistent with the crystal structure. On the other hand, the mononuclear Tb(III)-Pc complex exhibited only a single magnetic relaxation process. This is clear evidence that the magnetic relaxation mechanism depends heavily on the dipole-dipole (f-f) interactions between the Tb(3+) ions in the dinuclear systems. Furthermore, the SMM behaviour of dinuclear Dy(III)-Pc type SMMs with smaller energy barriers compared with that of Tb(III)-Pc and slow-relaxation behaviour was explained. Dinuclear Dy(III)-Pc SMMs exhibited single-component magnetic relaxation behaviour. The results indicate that the magnetic relaxation properties of dinuclear Ln(III)-Pc multiple-decker complexes are affected by the local molecular symmetry and are extremely sensitive to tiny distortions in the coordination geometry. In other words, the spatial arrangement of the Ln(3+) ions (f-f interactions) in the crystal is important. Our work shows that the SMM properties can be fine-tuned by introducing weak intermolecular magnetic interactions in a controlled SMM spatial arrangement.

Hydrogen bonded binary molecular adducts derived from exobidentate N-donor ligand with dicarboxylic acids: Acid⋯imidazole hydrogen-bonding interactions in neutral and ionic heterosynthons

NASA Astrophysics Data System (ADS)

Kathalikkattil, Amal Cherian; Damodaran, Subin; Bisht, Kamal Kumar; Suresh, Eringathodi

2011-01-01

Four new binary molecular compounds between a flexible exobidentate N-heterocycle and a series of dicarboxylic acids have been synthesized. The N-donor 1,4-bis(imidazol-1-ylmethyl)benzene (bix) was reacted with flexible and rigid dicarboxylic acids viz., cyclohexane-1,4-dicarboxylic acid (H 2chdc), naphthalene-1,4-dicarboxylic acid (H 2npdc) and 1H-pyrazole-3,5-dicarboxylic acid (H 2pzdc), generating four binary molecular complexes. X-ray crystallographic investigation of the molecular adducts revealed the primary intermolecular interactions carboxylic acid⋯amine (via O-H⋯N) as well as carboxylate⋯protonated amine (via N-H +⋯O -) within the binary compounds, generating layered and two-dimensional sheet type H-bonded networks involving secondary weak interactions (C-H⋯O) including the solvent of crystallization. Depending on the differences in p Ka values of the selected base/acid (Δp Ka), diverse H-bonded supramolecular assemblies could be premeditated. This study demonstrates the H-bonding interactions between imidazole/imidazolium cation and carboxylic acid/carboxylate anion in providing sufficient driving force for the directed assembly of binary molecular complexes. In the two-component solid form of hetero synthons involving bix and dicarboxylic acid, only H 2chdc exist as cocrystal with bix, while all the other three compounds crystallized exclusively as salt, in agreement with the Δp Ka values predicted for the formation of salts/cocrystals from the base and acid used in the synthesis of supramolecular solids.

Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

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

Lichtenberger, D.L.

1991-10-01

The formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies has been developed into a single equation which unifies the treatment of covalent bonds, ionic bonds, and partially ionic bonds. This relationship has been used to clarify the fundamental thermodynamic information relating to metal-hydrogen, metal-alkyl, and metal-metal bond energies. We have been able to obtain a direct observation and measurement of the stabilization energy provided by the agostic interaction of the C-H bond with the metal. The ionization energies have also been used to correlate the rates of carbonyl substitution reactions of ({eta}{sup 5}-C{sub 5}H{sub 4}X)Rh(CO){sub 2}more » complexes, and to reveal the electronic factors that control the stability of the transition state. The extent that the electronic features of these bonding interactions transfer to other chemical systems is being investigated in terms of the principle of additivity of ligand electronic effects. Specific examples under study include metal- phosphines, metal-halides, and metallocenes. Especially interesting has been the recent application of these techniques to the characterization of the soccer-ball shaped C{sub 60} molecule, buckminsterfullerene, and its interaction with a metal surface. The high-resolution valence ionizations in the gas phase reveal the high symmetry of the molecule, and studies of thin films of C{sub 60} reveal weak intermolecular interactions. Scanning tunneling and atomic force microscopy reveal the arrangement of spherical molecules on gold substrates, with significant delocalization of charge from the metal surface. 21 refs.« less

Local structural ordering in surface-confined liquid crystals

NASA Astrophysics Data System (ADS)

Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

2017-06-01

The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

Crystal structure of the Leishmania major peroxidase–cytochrome c complex

PubMed Central

Jasion, Victoria S.; Doukov, Tzanko; Pineda, Stephanie H.; Li, Huiying; Poulos, Thomas L.

2012-01-01

The causative agent of leishmaniasis is the protozoan parasite Leishmania major. Part of the host protective mechanism is the production of reactive oxygen species including hydrogen peroxide. In response, L. major produces a peroxidase, L. major peroxidase (LmP), that helps to protect the parasite from oxidative stress. LmP is a heme peroxidase that catalyzes the peroxidation of mitochondrial cytochrome c. We have determined the crystal structure of LmP in a complex with its substrate, L. major cytochrome c (LmCytc) to 1.84 Å, and compared the structure to its close homolog, the yeast cytochrome c peroxidase–cytochrome c complex. The binding interface between LmP and LmCytc has one strong and one weak ionic interaction that the yeast system lacks. The differences between the steady-state kinetics correlate well with the Lm redox pair being more dependent on ionic interactions, whereas the yeast redox pair depends more on nonpolar interactions. Mutagenesis studies confirm that the ion pairs at the intermolecular interface are important to both kcat and KM. Despite these differences, the electron transfer path, with respect to the distance between hemes, along the polypeptide chain is exactly the same in both redox systems. A potentially important difference, however, is the side chains involved. LmP has more polar groups (Asp and His) along the pathway compared with the nonpolar groups (Leu and Ala) in the yeast system, and as a result, the electrostatic environment along the presumed electron transfer path is substantially different. PMID:23100535

Study on four polymorphs of bifendate based on X-ray crystallography.

PubMed

Nie, Jinju; Yang, Dezhi; Hu, Kun; Lu, Yang

2016-05-01

Bifendate, a synthetic anti-hepatitis drug, exhibits polycrystalline mode phenomena with 2 polymorphs reported (forms A and B). Single crystals of the known crystalline form B and 3 new crystallosolvates involving bifendate solvated with tetrahydrofuran (C), dioxane (D), and pyridine (E) in a stoichiometric ratio of 1:1 were obtained and characterized by X-ray crystallography, thermal analysis, and Fourier transform infrared (FT-IR) spectroscopy. The differences in molecular conformation, intermolecular interaction and crystal packing arrangement for the four polymorphs were determined and the basis for the polymorphisms was investigated. The rotation of single bonds resulted in different orientations for the biphenyl, methyl ester and methoxyl groups. All guest solvent molecules interacted with the host molecule via an interesting intercalative mode along the [1 0 0] direction in the channel formed by the host molecules through weak aromatic stacking interactions or non-classical hydrogen bonds, of which the volume and planarity played an important role in the intercalation of the host with the guest. The incorporation of solvent-augmented rotation of the C-C bond of the biphenyl group had a striking effect on the host molecular conformation and contributed to the formation of bifendate polymorphs. Moreover, the simulated powder X-ray diffraction (PXRD) patterns for each form were calculated on the basis of the single-crystal data and proved to be unique. The single-crystal structures of the four crystalline forms are reported in this paper.

Beta-Strand Interfaces of Non-Dimeric Protein Oligomers Are Characterized by Scattered Charged Residue Patterns

PubMed Central

Feverati, Giovanni; Achoch, Mounia; Zrimi, Jihad; Vuillon, Laurent; Lesieur, Claire

2012-01-01

Protein oligomers are formed either permanently, transiently or even by default. The protein chains are associated through intermolecular interactions constituting the protein interface. The protein interfaces of 40 soluble protein oligomers of stœchiometries above two are investigated using a quantitative and qualitative methodology, which analyzes the x-ray structures of the protein oligomers and considers their interfaces as interaction networks. The protein oligomers of the dataset share the same geometry of interface, made by the association of two individual β-strands (β-interfaces), but are otherwise unrelated. The results show that the β-interfaces are made of two interdigitated interaction networks. One of them involves interactions between main chain atoms (backbone network) while the other involves interactions between side chain and backbone atoms or between only side chain atoms (side chain network). Each one has its own characteristics which can be associated to a distinct role. The secondary structure of the β-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular β-sheets (MCWIV). The intermolecular specificity is provided by the side chain networks via positioning different types of charged residues at the extremities (arginine) and in the middle (glutamic acid and histidine) of the interface. Such charge distribution helps discriminating between sequences of intermolecular β-strands, of intramolecular β-strands and of β-strands forming β-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the β-strands of the cholera toxin B subunit interface, when produced individually as synthetic peptides, are capable of inhibiting the assembly of the toxin into pentamers. Thus, their sequences contain the features necessary for a β-interface formation. Such β-strands could be considered as ‘assemblons’, independent associating units, by homology to the foldons (independent folding unit). Such property would be extremely valuable in term of assembly inhibitory drug development. PMID:22496732

The mechanism of interaction of polymethacrylic acid with sodium dodecylbenzenesulfonate in aqueous solutions

NASA Astrophysics Data System (ADS)

Sachko, A. V.; Zakordonskii, V. P.; Voloshinovskii, A. S.; Golod, T. Yu.

2009-07-01

A complex of physicochemical methods (light scattering, potentiometry, conductometry, viscometry, tensiometry, and fluorescence spectroscopy) were used to show the possibility of formation of intermolecular associates/complexes in systems with likely charged components. The driving forces of such interactions were analyzed and a possible scheme of complex formation between polymethacrylic acid and sodium dodecylbenzenesulfonate was suggested.

Intermolecular interactions and substrate effects for an adamantane monolayer on a Au(111) surface

NASA Astrophysics Data System (ADS)

Sakai, Yuki; Nguyen, Giang D.; Capaz, Rodrigo B.; Coh, Sinisa; Pechenezhskiy, Ivan V.; Hong, Xiaoping; Wang, Feng; Crommie, Michael F.; Saito, Susumu; Louie, Steven G.; Cohen, Marvin L.

2013-12-01

We study theoretically and experimentally the infrared (IR) spectrum of an adamantane monolayer on a Au(111) surface. Using a STM-based IR spectroscopy technique (IRSTM) we are able to measure both the nanoscale structure of an adamantane monolayer on Au(111) as well as its infrared spectrum, while DFT-based ab initio calculations allow us to interpret the microscopic vibrational dynamics revealed by our measurements. We find that the IR spectrum of an adamantane monolayer on Au(111) is substantially modified with respect to the gas-phase IR spectrum. The first modification is caused by the adamantane-adamantane interaction due to monolayer packing, and it reduces the IR intensity of the 2912 cm-1 peak (gas phase) by a factor of 3.5. The second modification originates from the adamantane-gold interaction, and it increases the IR intensity of the 2938 cm-1 peak (gas phase) by a factor of 2.6 and reduces its frequency by 276 cm-1. We expect that the techniques described here can be used for an independent estimate of substrate effects and intermolecular interactions in other diamondoid molecules and for other metallic substrates.

Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases

NASA Astrophysics Data System (ADS)

Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

2015-04-01

Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases.

Book Review: Near infrared surface-enhanced Raman spectroscopic study of antiretroviraly drugs hypericin and emodin in aqueous silver colloids

NASA Astrophysics Data System (ADS)

Sánchez-Cortés, S.; Jancura, D.; Miskovsky, P.; Bertoluzza, A.

1997-05-01

The near infrared surface-enhanced Raman spectra (NIR SERS) of antiretroviraly drugs hypericin and its analogs emodin and bianthrone were studied at different drug concentration, dimethylsulfoxide concentration, pH and time. The differences observed in the SERS spectra when varying some of these parameters are attributed to changes in the adsorbate coverage and orientation of these molecules on the silver colloids, and can be related to the monomeric drug concentration existing in the solution. Two different drug orientations on the metal surface can be deduced: perpendicular and planar, which can be characterized by two different SERS profiles. The drug reorientation on the surface is indicative of a change in the oligomer-monomer equilibrium in the solution, what implies that the SERS technique can be used as an indirect method to monitor the intermolecular interactions of these molecules in water. In addition the UV-visible absorption spectra of these drugs also reveals the existence of intermolecular interactions in water and the temperature dependence of these interactions.

The simulation study of protein-protein interfaces based on the 4-helix bundle structure

NASA Astrophysics Data System (ADS)

Fukuda, Masaki; Komatsu, Yu; Morikawa, Ryota; Miyakawa, Takeshi; Takasu, Masako; Akanuma, Satoshi; Yamagishi, Akihiko

2013-02-01

Docking of two protein molecules is induced by intermolecular interactions. Our purposes in this study are: designing binding interfaces on the two proteins, which specifically interact to each other; and inducing intermolecular interactions between the two proteins by mixing them. A 4-helix bundle structure was chosen as a scaffold on which binding interfaces were created. Based on this scaffold, we designed binding interfaces involving charged and nonpolar amino acid residues. We performed molecular dynamics (MD) simulation to identify suitable amino acid residues for the interfaces. We chose YciF protein as the scaffold for the protein-protein docking simulation. We observed the structure of two YciF protein molecules (I and II), and we calculated the distance between centroids (center of gravity) of the interfaces' surface planes of the molecules I and II. We found that the docking of the two protein molecules can be controlled by the number of hydrophobic and charged amino acid residues involved in the interfaces. Existence of six hydrophobic and five charged amino acid residues within an interface were most suitable for the protein-protein docking.

Intermolecular Interactions and the Viscosity of Highly Concentrated Monoclonal Antibody Solutions.

PubMed

Binabaji, Elaheh; Ma, Junfen; Zydney, Andrew L

2015-09-01

The large increase in viscosity of highly concentrated monoclonal antibody solutions can be challenging for downstream processing, drug formulation, and delivery steps. The objective of this work was to examine the viscosity of highly concentrated solutions of a high purity IgG1 monoclonal antibody over a wide range of protein concentrations, solution pH, ionic strength, and in the presence / absence of different excipients. Experiments were performed with an IgG1 monoclonal antibody provided by Amgen. The steady-state viscosity was evaluated using a Rheometrics strain-controlled rotational rheometer with a concentric cylinder geometry. The viscosity data were well-described by the Mooney equation. The data were analyzed in terms of the antibody virial coefficients obtained from osmotic pressure data evaluated under the same conditions. The viscosity coefficient in the absence of excipients was well correlated with the third osmotic virial coefficient, which has a negative value (corresponding to short range attractive interactions) at the pH and ionic strength examined in this work. These results provide important insights into the effects of intermolecular protein-protein interactions on the behavior of highly concentrated antibody solutions.

Quaterrylene molecules on Ag(111): self-assembly behavior and voltage pulse induced trimer formation.

PubMed

He, Yangyong; Cai, Zeying; Shao, Jian; Xu, Li; She, Limin; Zheng, Yue; Zhong, Dingyong

2018-05-03

The self-assembly behavior of quaterrylene (QR) molecules on Ag(111) surfaces has been investigated by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. It is found that the QR molecules are highly mobile on the Ag(111) surface at 78 K. No ordered assembled structure is formed on the surface with a sub-monolayer coverage up to 0.8 monolayer due to the intermolecular repulsive interactions, whereas ordered molecular structures are observed at one monolayer coverage. According to our DFT calculations, charge transfer occurs between the substrate and the adsorbed QR molecule. As a result, out-of-plane dipoles appear at the interface, which are ascribed to the repulsive dipole-dipole interactions between the QR molecules. Furthermore, due to the planar geometry, the QR molecules exhibit relatively low diffusion barriers on Ag(111). By applying a voltage pulse between the tunneling gap, immobilization and aggregation of QR molecules take place, resulting in the formation of a triangle-shaped trimer. Our work demonstrates the ability of manipulating intermolecular repulsive and attractive interactions at the single molecular level.

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

PubMed

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

PubMed

Mondal, Pradip Kumar; Yadav, Hare Ram; Choudhury, Angshuman Roy; Chopra, Deepak

2017-10-01

Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp 2 -H...F-Csp 2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp 2 -F...F-Csp 2 contacts.

Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides* #

PubMed Central

Yu, Hua; Wang, Mao-Jun; Xuan, Nan-Xia; Shang, Zhi-Cai; Wu, Jun

2015-01-01

Objective: To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Methods: Molecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. Results: The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding. Conclusions: van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues. PMID:26465136

Interactions of ionic liquids and acetone: thermodynamic properties, quantum-chemical calculations, and NMR analysis.

PubMed

Ruiz, Elia; Ferro, Victor R; Palomar, Jose; Ortega, Juan; Rodriguez, Juan Jose

2013-06-20

The interactions between ionic liquids (ILs) and acetone have been studied to obtain a further understanding of the behavior of their mixtures, which generally give place to an exothermic process, mutual miscibility, and negative deviation of Raoult's law. COSMO-RS was used as a suitable computational method to systematically analyze the excess enthalpy of IL-acetone systems (>300), in terms of the intermolecular interactions contributing to the mixture behavior. Spectroscopic and COSMO-RS results indicated that acetone, as a polar compound with strong hydrogen bond acceptor character, in most cases, establishes favorable hydrogen bonding with ILs. This interaction is strengthened by the presence of an acidic cation and an anion with dispersed charge and non-HB acceptor character in the IL. COSMO-RS predictions indicated that gas-liquid and vapor-liquid equilibrium data for IL-acetone systems can be finely tuned by the IL selection, that is, acting on the intermolecular interactions between the molecular and ionic species in the liquid phase. NMR measurements for IL-acetone mixtures at different concentrations were also carried out. Quantum-chemical calculations by using molecular clusters of acetone and IL species were finally performed. These results provided additional evidence of the main role played by hydrogen bonding in the behavior of systems containing ILs and HB acceptor compounds, such as acetone.

Calculating Henry’s Constants of Charged Molecules Using SPARC

EPA Science Inventory

SPARC Performs Automated Reasoning in Chemistry is a computer program designed to model physical and chemical properties of molecules solely based on thier chemical structure. SPARC uses a toolbox of mechanistic perturbation models to model intermolecular interactions. SPARC has ...

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

DOE PAGES

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

2017-04-11

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contactsmore » for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP(r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.« less

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

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

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contactsmore » for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP(r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.« less

Theoretical analysis of the formation driving force and decreased sensitivity for CL-20 cocrystals

NASA Astrophysics Data System (ADS)

Zhou, Jun-Hong; Shi, Liang-Wei; Zhang, Chao-Yang; Li, Hong-Zhen; Chen, Min-Bo; Chen, Wei-Ming

2016-07-01

Methods that analyze the driving force in the formation of the new energetic cocrystal are proposed in this paper. Various intermolecular interactions in the 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazatetracyclo [5.5.0.05,9.03,11]dodecane (CL-20) cocrystals are compared with those in pure CL-20 and coformer crystals by atom in molecule (AIM) and Hirshfeld surface methods under the supramolecular cluster model. The driving force in the formation of the CL-20 cocrystals is analyzed. The main driving force in the formation of the cocrystal CL-20/HMX comes from the O···H interactions, that in the formation of the cocrystal CL-20/TNT from the O···H and C···O interactions, and that in the formation of the cocrystal CL-20/BTF from the N···H and N···O interactions. Other interactions in the CL-20 cocrystals only contribute to their stabilization. At the same time, the reasons for the decreased impact sensitivity of the CL-20 cocrystals are also analyzed. They are the strengthening of the intermolecular interactions, the reducing of the free space, and the changing of the surrounding of CL-20 molecule in the CL-20 cocrystals in comparison with those in the pure CL-20 crystal.

Local Structure of Ion Pair Interaction in Lapatinib Amorphous Dispersions characterized by Synchrotron X-Ray diffraction and Pair Distribution Function Analysis

NASA Astrophysics Data System (ADS)

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

2017-04-01

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contacts for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Finally, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (Δ) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.

A surface plasmon resonance study of the intermolecular interaction between Escherichia coli topoisomerase I and pBAD/Thio supercoiled plasmid DNA

PubMed Central

Tiwari, Purushottam Babu; Annamalai, Thirunavukkarasu; Cheng, Bokun; Narula, Gagandeep; Wang, Xuewen; Tse-Dinh, Yuk-Ching; He, Jin; Darici, Yesim

2014-01-01

To date, the bacterial DNA topoisomerases are one of the major target biomolecules for the discovery of new antibacterial drugs. DNA topoisomerase regulates the topological state of DNA, which is very important for replication, transcription and recombination. The relaxation of negatively supercoiled DNA is catalyzed by bacterial DNA topoisomerase I (topoI) and this reaction requires Mg2+. In this report, we first quantitatively studied the intermolecular interactions between Escherichia coli topoisomerase I (EctopoI) and pBAD/Thio supercoiled plasmid DNA using surface plasmon resonance (SPR) technique. The equilibrium dissociation constant (Kd) for EctopoI-pBAD/Thio interactions is determined to be about 8 nM. We then studied the effect of Mg2+ on the catalysis of EctopoI-pBAD/Thio reaction. A slightly higher equilibrium dissociation constant (~15 nM) was obtained for Mg2+ coordinated EctopoI (Mg2+EctopoI)-pBAD/Thio interactions. In addition, we observed a larger dissociation rate constant (kd) for Mg2+EctopoI-pBAD/Thio interactions (~0.043 s−1), compared to EctopoI-pBAD/Thio interactions (~0.017 s−1). These results suggest that enzyme turnover during plasmid DNA relaxation is enhanced due to the presence of Mg2+ and furthers the understanding of importance of the Mg2+ ion for bacterial topoisomerase I catalytic activity. PMID:24530905

Interlocking Molecular Gear Chains Built on Surfaces.

PubMed

Zhao, Rundong; Qi, Fei; Zhao, Yan-Ling; Hermann, Klaus E; Zhang, Rui-Qin; Van Hove, Michel A

2018-05-17

Periodic chains of molecular gears in which molecules couple with each other and rotate on surfaces have been previously explored by us theoretically using ab initio simulation tools. On the basis of the knowledge and experience gained about the interactions between neighboring molecular gears, we here explore the transmission of rotational motion and energy over larger distances, namely, through a longer chain of gear-like passive "slave" molecules. Such microscopic gears exhibit quite different behaviors compared to rigid cogwheels in the macroscopic world due to their structural flexibility affecting intermolecular interaction. Here, we investigate the capabilities of such gear chains and reveal the mechanisms of the transmission process in terms of both quantum-level density functional theory (DFT) and simple classical mechanics. We find that the transmission of rotation along gear chains depends strongly on the gear-gear distance: short distances can cause tilting of gears and even irregular "creep-then-jump" (or "stick-slip") motion or expulsion of gears; long gear-gear distances cause weak coupling between gears, slipping and skipping. More importantly, for transmission of rotation at intermediate gear-gear distances, our modeling clearly exhibits the relative roles of several important factors: flexibility of gear arms, axles, and supports, as well as resulting rotational delays, slippages, and thermal and other effects. These studies therefore allow better informed design of future molecular machine components involving motors, gears, axles, etc.

Thermodynamic aspects of cluster crystallization in cryoprotective solutions.

PubMed

Osetsky, A I

2011-01-01

Crystallization of the solutions with quite a high intermolecular interaction of the components is analyzed. For the first time there has been considered the phenomenon of cluster crystallization of these solutions, enabling the reduction of total energy of intermolecular bonds, broken down during crystallization of the components has been discussed. A special priority is given to the cluster crystallization of aqueous solutions of cryoprotective substances close to vitrification temperature. Within this temperature range the mechanism of cluster crystallization is especially effective due to a sharp reduction of sizes of critical ice nucleation centers and diffusion mobility of molecules. This should be taken into account when designing the cryopreservation protocols for biological systems.

Insight into the structure of photosynthetic LH2 aggregate from spectroscopy simulations.

PubMed

Rancova, Olga; Sulskus, Juozas; Abramavicius, Darius

2012-07-12

Using the electrostatic model of intermolecular interactions, we obtain the Frenkel exciton Hamiltonian parameters for the chlorophyll Qy band of a photosynthetic peripheral light harvesting complex LH2 of a purple bacteria Rhodopseudomonas acidophila from structural data. The intermolecular couplings are mostly determined by the chlorophyll relative positions, whereas the molecular transition energies are determined by the background charge distribution of the whole complex. The protonation pattern of titratable residues is used as a tunable parameter. By studying several protonation state scenarios for distinct protein groups and comparing the simulated absorption and circular dichroism spectra to experiment, we determine the most probable configuration of the protonation states of various side groups of the protein.

Energetics and electronic structures of chemically decorated C60 chains

NASA Astrophysics Data System (ADS)

Furutani, Sho; Okada, Susumu

2018-06-01

We studied the energetics and electronic structures of one-dimensional molecular chains of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) using the density functional theory (DFT). Our DFT calculations show that the binding energies of PCBM range from 90 to 300 meV, depending on not only the intermolecular spacing but also the intermolecular arrangements owing to the interaction between functional groups and C60. The electronic structure of PCBM chains are also sensitive to the mutual arrangements of PCBM in their chain structure. The calculated effective masses of the conduction band range from 0.58 to 634.97m e, giving rise to anisotropic transport properties in their condensed phase.

Electronic, structural and chemical effects of charge-transfer at organic/inorganic interfaces

NASA Astrophysics Data System (ADS)

Otero, R.; Vázquez de Parga, A. L.; Gallego, J. M.

2017-07-01

During the last decade, interest on the growth and self-assembly of organic molecular species on solid surfaces spread over the scientific community, largely motivated by the promise of cheap, flexible and tunable organic electronic and optoelectronic devices. These efforts lead to important advances in our understanding of the nature and strength of the non-bonding intermolecular interactions that control the assembly of the organic building blocks on solid surfaces, which have been recently reviewed in a number of excellent papers. To a large extent, such studies were possible because of a smart choice of model substrate-adsorbate systems where the molecule-substrate interactions were purposefully kept low, so that most of the observed supramolecular structures could be understood simply by considering intermolecular interactions, keeping the role of the surface always relatively small (although not completely negligible). On the other hand, the systems which are more relevant for the development of organic electronic devices include molecular species which are electron donors, acceptors or blends of donors and acceptors. Adsorption of such organic species on solid surfaces is bound to be accompanied by charge-transfer processes between the substrate and the adsorbates, and the physical and chemical properties of the molecules cannot be expected any longer to be the same as in solution phase. In recent years, a number of groups around the world have started tackling the problem of the adsorption, self- assembly and electronic and chemical properties of organic species which interact rather strongly with the surface, and for which charge-transfer must be considered. The picture that is emerging shows that charge transfer can lead to a plethora of new phenomena, from the development of delocalized band-like electron states at molecular overlayers, to the existence of new substrate-mediated intermolecular interactions or the strong modification of the chemical reactivity of the adsorbates. The aim of this review is to start drawing general conclusions and developing new concepts which will help the scientific community to proceed more efficiently towards the understanding of organic/inorganic interfaces in the strong interaction limit, where charge-transfer effects must be taken into consideration.

An approach to the origin of self-replicating system. I - Intermolecular interactions

NASA Technical Reports Server (NTRS)

Macelroy, R. D.; Coeckelenbergh, Y.; Rein, R.

1978-01-01

The present paper deals with the characteristics and potentialities of a recently developed computer-based molecular modeling system. Some characteristics of current coding systems are examined and are extrapolated to the apparent requirements of primitive prebiological coding systems.

Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

PubMed

Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

2014-12-11

The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

NASA Technical Reports Server (NTRS)

Crawford, Lisa; Karr, Laurel J.; Nadarajah, Arunan; Pusey, Marc

1999-01-01

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 43 axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to (3)500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 (Registered) PHE or ALA and ASN 113 (Registered) ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 43 helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Tetragonal Lysozyme Interactions Studied by Site Directed Mutagenesis

NASA Technical Reports Server (NTRS)

Crawford, Lisa; Karr, Laurel; Pusey, Marc

1998-01-01

A number of recent experimental and theoretical studies have indicated that tetragonal lysozyme crystal growth proceeds by the addition of aggregates, formed by reversible self association of the solute molecules in the bulk'solution. Periodic bond chain and atomic force microscopy studies have indicated that the probable growth unit is at minimum a 43 tetramer, and most likely an octamer composed of two complete turns about the 4(sub 3) axis. If these results are correct, then there are intermolecular interactions which are only formed in the solution and others only formed at the joining of the growth unit to the crystal surface. We have set out to study these interactions, and the correctness of this hypothesis, using site directed mutagenesis of specific amino acid residues involved in the different bonds. We had initially expressed wild type lysozyme in S. cervasiae with yields of approximately 5 mg/L, which were eventually raised to approximately 40 mg/L. We are now moving the expression to the Pichia system, with anticipated yields of 300 to greater than 500 mg/L, comparable to what can be obtained from egg whites. An additional advantage of using recombinant protein is the greater genetic homogeneity of the material obtained and the absence of any other contaminating egg proteins. The first mutation experiments are TYR 23 yields PHE or ALA and ASN 113 yields ALA or ASP. Both TYR 23 and ASN 113 form part of the postulated dimerization intermolecular binding site which lead to the formation of the 4(sub 3) helix. Tyrosine also participates in an intermolecular hydrogen bond with ARG 114. The results of these and subsequent experiments will be discussed.

Rational design of viscosity reducing mutants of a monoclonal antibody: Hydrophobic versus electrostatic inter-molecular interactions

PubMed Central

Nichols, Pilarin; Li, Li; Kumar, Sandeep; Buck, Patrick M; Singh, Satish K; Goswami, Sumit; Balthazor, Bryan; Conley, Tami R; Sek, David; Allen, Martin J

2015-01-01

High viscosity of monoclonal antibody formulations at concentrations ≥100 mg/mL can impede their development as products suitable for subcutaneous delivery. The effects of hydrophobic and electrostatic intermolecular interactions on the solution behavior of MAB 1, which becomes unacceptably viscous at high concentrations, was studied by testing 5 single point mutants. The mutations were designed to reduce viscosity by disrupting either an aggregation prone region (APR), which also participates in 2 hydrophobic surface patches, or a negatively charged surface patch in the variable region. The disruption of an APR that lies at the interface of light and heavy chain variable domains, VH and VL, via L45K mutation destabilized MAB 1 and abolished antigen binding. However, mutation at the preceding residue (V44K), which also lies in the same APR, increased apparent solubility and reduced viscosity of MAB 1 without sacrificing antigen binding or thermal stability. Neutralizing the negatively charged surface patch (E59Y) also increased apparent solubility and reduced viscosity of MAB 1, but charge reversal at the same position (E59K/R) caused destabilization, decreased solubility and led to difficulties in sample manipulation that precluded their viscosity measurements at high concentrations. Both V44K and E59Y mutations showed similar increase in apparent solubility. However, the viscosity profile of E59Y was considerably better than that of the V44K, providing evidence that inter-molecular interactions in MAB 1 are electrostatically driven. In conclusion, neutralizing negatively charged surface patches may be more beneficial toward reducing viscosity of highly concentrated antibody solutions than charge reversal or aggregation prone motif disruption. PMID:25559441

Theoretical insights into the structures and mechanical properties of HMX/NQ cocrystal explosives and their complexes, and the influence of molecular ratios on their bonding energies.

PubMed

Li, Yong-Xiang; Chen, Shu-Sen; Ren, Fu-de

2015-09-01

Molecular dynamics (MD) methods were employed to study the binding energies and mechanical properties of selected crystal planes of 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)/nitroguanidine (NQ) cocrystals at different molecular molar ratios. The densities and detonation velocities of the cocrystals at different molar ratios were estimated. The intermolecular interaction and bond dissociation energy (BDE) of the N-NO2 bond in the HMX:NQ (1:1) complex were calculated using the B3LYP, MP2(full) and M06-2X methods with the 6-311++G(d,p) and 6-311++G(2df,2p) basis sets. The results indicated that the HMX/NQ cocrystal prefers cocrystalizing in a 1:1 molar ratio, and the cocrystallization is dominated by the (0 2 0) and (1 0 0) facets. The K, G, and E values of the ratio of 1:1 are smaller than those of the other ratios, and the 1:1 cocrystal has the best ductility. The N-NO2 bond becomes stronger upon the formation of the intermolecular H-bonding interaction and the sensitivity of HMX decreases in the cocrystal. This sensitivity change in the HMX/NQ cocrystal originates not only from the formation of the intermolecular interaction but also from the increment of the BDE of N-NO2 bond in comparison with isolated HMX. The HMX/NQ (1:1) cocrystal exhibits good detonation performance. Reduced density gradient (RDG) reveals the nature of cocrystallization. Analysis of the surface electrostatic potential further confirmed that the sensitivity decreases in complex (or cocrystal) in comparison with that in isolated HMX.

Rational design of viscosity reducing mutants of a monoclonal antibody: hydrophobic versus electrostatic inter-molecular interactions.

PubMed

Nichols, Pilarin; Li, Li; Kumar, Sandeep; Buck, Patrick M; Singh, Satish K; Goswami, Sumit; Balthazor, Bryan; Conley, Tami R; Sek, David; Allen, Martin J

2015-01-01

High viscosity of monoclonal antibody formulations at concentrations ≥100 mg/mL can impede their development as products suitable for subcutaneous delivery. The effects of hydrophobic and electrostatic intermolecular interactions on the solution behavior of MAB 1, which becomes unacceptably viscous at high concentrations, was studied by testing 5 single point mutants. The mutations were designed to reduce viscosity by disrupting either an aggregation prone region (APR), which also participates in 2 hydrophobic surface patches, or a negatively charged surface patch in the variable region. The disruption of an APR that lies at the interface of light and heavy chain variable domains, VH and VL, via L45K mutation destabilized MAB 1 and abolished antigen binding. However, mutation at the preceding residue (V44K), which also lies in the same APR, increased apparent solubility and reduced viscosity of MAB 1 without sacrificing antigen binding or thermal stability. Neutralizing the negatively charged surface patch (E59Y) also increased apparent solubility and reduced viscosity of MAB 1, but charge reversal at the same position (E59K/R) caused destabilization, decreased solubility and led to difficulties in sample manipulation that precluded their viscosity measurements at high concentrations. Both V44K and E59Y mutations showed similar increase in apparent solubility. However, the viscosity profile of E59Y was considerably better than that of the V44K, providing evidence that inter-molecular interactions in MAB 1 are electrostatically driven. In conclusion, neutralizing negatively charged surface patches may be more beneficial toward reducing viscosity of highly concentrated antibody solutions than charge reversal or aggregation prone motif disruption.

Characterization of Intermolecular Interactions at Play in the 2,2,2-TRIFLUOROETHANOL Trimers Using Cavity and Chirped-Pulse Microwave Spectroscopy

NASA Astrophysics Data System (ADS)

Seifert, Nathan A.; Thomas, Javix; Jäger, Wolfgang; Xu, Yunjie

2017-06-01

2,2,2-trifluoroethanol (TFE) is a common aqueous co-solvent in biological chemistry which may induce or destabilize secondary structures of proteins and polypeptides, thanks to its diverse intermolecular linkages originating from the hydrogen bonding potential of both the hydroxyl and perfluoro groups. Theoretically, the TFE monomer is predicted to have two stable gauche (gauche^{+}/gauche^{-}) conformations whereas the trans form is unstable or is supported only by a very shallow potential. Only the gauche conformers have been identified in the gas phase, whereas liquid phase studies suggest a trans:gauche ratio of 2:3. The question at which sample (cluster) size the trans form of TFE would appear was one major motivation for our study. Here, we report the detection of three trimers of TFE using Balle-Flygare cavity and chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) techniques. The most stable observed trimer features one trans- and two gauche-TFE subunits. The other two trimers, observed using a newly constructed 2-6 GHz CP-FTMW spectrometer, consist of only the two gauche conformers of TFE. Quantum Theory of Atoms in Molecules (QTAIM) and non-covalent interactions (NCI) analyses give detailed insights into which intermolecular interactions are at play to stabilize the trans form of TFE in the most stable trimer. M. Buck, Q. Rev. Biophys. 1998, 31, 297-335. I. Bakó, T. Radnai, M. Claire, B. Funel, J. Chem. Phys. 2004, 121, 12472-12480. R. F. W. Bader, Chem. Rev. 1991, 91, 893-928. E. R. Johnson, S. Keinan, P. Mori-Sánchez, J. Contreras-Garcia, A. J. Cohen, W. Yang, J. Am. Chem. Soc., 2010, 132, 6498-6506.

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

NASA Astrophysics Data System (ADS)

Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N.; Schnier, Paul D.; Klassen, John S.

2014-05-01

This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 105 M-1] is similar to the value for the PA [(3.8 ± 0.1) × 105 M-1]; Ka for 3-OHPA [(1.1 ± 0.3) × 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

Theoretical predictions of vibration-rotation-tunneling dynamics of the weakly bound trimer (H 2O) 2HCl

NASA Astrophysics Data System (ADS)

Struniewicz, Cezary; Korona, Tatiana; Moszynski, Robert; Milet, Anne

2001-08-01

In this Letter we report a theoretical study of the vibration-rotation-tunneling (VRT) states of the (H 2O) 2HCl trimer. Five degrees of freedom are considered: two angles corresponding to the torsional (flipping) motions of the free, non-hydrogen-bonded, hydrogen atoms in the complex, and three angles describing the overall rotation of the trimer in the space. A two-dimensional potential energy surface is generated ab initio by symmetry-adapted perturbation theory (SAPT). Tunneling splittings, frequencies of the intermolecular vibrations, and vibrational line strengths of spectroscopic transitions are predicted.

Modeling interactions between a β-O-4 type lignin model compound and 1-allyl-3-methylimidazolium chloride ionic liquid.

PubMed

Zhu, Youtao; Yan, Jing; Liu, Chengbu; Zhang, Dongju

2017-08-01

Aiming at understanding the molecular mechanism of the lignin dissolution in imidazolium-based ionic liquids (ILs), this work presents a combined quantum chemistry (QC) calculation and molecular dynamics (MD) simulation study on the interaction of the lignin model compound, veratrylglycerol-β-guaiacyl ether (VG) with 1-allyl-3-methylimidazolium chloride ([Amim]Cl). The monomer of VG is shown to feature a strong intramolecular hydrogen bond, and its dimer is indicated to present important π-π stacking and intermolecular hydrogen bonding interactions. The interactions of both the cation and anion of [Amim]Cl with VG are shown to be stronger than that between the two monomers, indicating that [Amim]Cl is capable of dissolving lignin. While Cl - anion forms a hydrogen-bonded complex with VG, the imidazolium cation interacts with VG via both the π-π stacking and intermolecular hydrogen bonding. The calculated interaction energies between VG and the IL or its components (the cation, anion, and ion pair) indicate the anion plays a more important role than the cation for the dissolution of lignin in the IL. Theoretical results provide help for understanding the molecular mechanism of lignin dissolution in imidazolium-based IL. The theoretical calculations on the interaction between the lignin model compound and [Amim]Cl ionic liquid indicate that the anion of [Amim]Cl plays a more important role for lignin dissolution although the cation also makes a substantial contribution. © 2017 Wiley Periodicals, Inc.

High Pressure Optical Studies of the Thallous Halides and of Charge-Transfer Complexes

NASA Astrophysics Data System (ADS)

Jurgensen, Charles Willard

High pressure was used to study the insulator -to-metal transition in sulfur and the thallous halides and to study the intermolecular interactions in charge -transfer complexes. The approach to the band overlap insulator -to-metal transition was studied in three thallous halides and sulfur by optical absorption measurements of the band gap as a function of pressure. The band gap of sulfur continuously decreases with pressure up to the insulator -to-metal transition which occurs between 450 and 485 kbars. The results on the thallous halides indicate that the indirect gap decreases more rapidly than the direct gap; the closing of the indirect gap is responsible for the observed insulator -to-metal transitions. High pressure electronic and vibrational spectroscopic measurements on the solid-state complexes of HMB-TCNE were used to study the intermolecular interactions of charge -transfer complexes. The vibrational frequency shifts indicate that the degree of charge transfer increases with pressure which is independently confirmed by an increase in the molar absorptivity of the electronic charge-transfer peak. Induction and dispersion forces contribute towards a red shift of the charge-transfer peak; however, charge-transfer resonance contributes toward a blue shift and this effect is dominant for the HMB-TCNE complexes. High pressure electronic spectra were used to study the effect of intermolecular interactions on the electronic states of TCNQ and its complexes. The red shifts with pressure of the electronic spectra of TCNQ and (TCNQ)(' -) in polymer media and of crystalline TCNQ can be understood in terms of Van der Waals interactions. None of the calculations which considered intradimer distance obtained the proper behavior for either the charge-transfer of the locally excited states of the complexes. The qualitative behavior of both states can be interpreted as the effect of increased mixing of the locally excited and charge transfer states.

High rectification in organic diodes based on liquid crystalline phthalocyanines.

PubMed

Apostol, Petru; Eccher, Juliana; Dotto, Marta Elisa Rosso; Costa, Cassiano Batesttin; Cazati, Thiago; Hillard, Elizabeth A; Bock, Harald; Bechtold, Ivan H

2015-12-28

The optical and electrical properties of mesogenic metal-free and metalated phthalocyanines (PCs) with a moderately sized and regioregular alkyl periphery were investigated. In solution, the individualized molecules show fluorescence lifetimes of 4-6 ns in THF. When deposited as solid thin films the materials exhibit significantly shorter fluorescence lifetimes with bi-exponential decay (1.4-1.8 ns; 0.2-0.4 ns) that testify to the formation of aggregates viaπ-π intermolecular interactions. In diode structures, their pronounced columnar order outbalances the unfavorable planar alignment and leads to excellent rectification behavior. Field-dependent charge carrier mobilities are obtained from the J-V curves in the trap-limited space-charge-limited current regime and demonstrate that the metalated PCs display an improved electrical response with respect to the metal-free homologue. The excited-state lifetime characterization suggest that the π-π intermolecular interactions are stronger for the metal-free PC, confirming that the metallic centre plays an important role in the charge transport inside these materials.

Studies on the syntheses, structural characterization, antimicrobial-, and DPPH radical scavenging activity of the cocrystals caffeine:cinnamic acid and caffeine:eosin dihydrate

NASA Astrophysics Data System (ADS)

Suresh Kumar, G. S.; Seethalakshmi, P. G.; Bhuvanesh, N.; Kumaresan, S.

2013-10-01

Two organic cocrystals namely, caffeine:cinnamic acid [(caf)(ca)] (1) and caffeine:eosin dihydrate [(caf)(eos)]·2H2O (2) were synthesized and studied by FT-IR, TGA/DTA, and single crystal XRD. The crystal system of cocrystal 1 is triclinic with space group P-1 and Z = 2 and that of cocrystal 2 is monoclinic with space group P21/C and Z = 4. An imidazole-carboxylic acid synthon is observed in the cocrystal 1. The intermolecular hydrogen bond, O-H⋯N and π-π interactions play a major role in stabilizing 1 whereas the intermolecular hydrogen bonds, O-H⋯O, O-H⋯N, and intramolecular hydrogen bond, O-H⋯Br; along with π-π interactions together play a vital role in stabilizing the structure of 2. The antimicrobial- and DPPH radical scavenging activities of both the cocrystals were studied.

Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; ...

2016-06-23

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Sub-Micellar Concentration of Sodium Dodecyl Sulphate Prevents Thermal Denaturation Induced Aggregation of Plant Lectin, Jacalin.

PubMed

Lavanya, V; Anil Kumar, B; Jamal, Shazia; Khan, Md Khurshid Alam; Ahmed, Neesar

2017-02-01

The irreversible thermal unfolding of jacalin, the lectin purified from jackfruit seeds was accompanied by aggregation, where intermolecular interactions among the subunits are favoured over intramolecular interactions. The extent of aggregation increased as a function of temperature, time and protein concentration. The anionic surfactant, sodium dodecyl sulphate (SDS) significantly suppressed the formation of aggregates as observed by turbidity measurements and Rayleigh scattering assay. Moreover, far UV-CD spectra indicate that the protein β sheet transforms into α helical structure, when denatured in the presence of 3 mM SDS. Further, jacalin when heated in the presence of SDS partially retained the hemagglutination activity when jacalin-SDS mixture was diluted to 1:8 factor since 3 mM SDS was found to lyse the red blood cells. Thus, SDS only altered the aggregation behaviour of jacalin by preventing intermolecular hydrogen bonding among the exposed residues but did not completely stabilize the native conformation.

Natural polymer biocomposites produced from processing raw wood flour by severe shear deformation.

PubMed

Zhang, Xiaoqing; Wu, Xiaolin; Haryono, Hengky; Xia, Kenong

2014-11-26

Wood flour (WF) based natural polymer biocomposites were produced using the equal channel angular pressing (ECAP) technique. The wood particle structures were disrupted and the cellulose crystallinity was decreased while bulk materials were formed with continuous phase structures by the severe shear-deformation during ECAP. The mechanical properties of the processed WF materials were enhanced when the processing temperature was increased due to enhanced intermolecular interactions and thermal crosslinking reactions among WF components. The processing capability was improved by using wheat gluten (WG) as additives, leading to significantly reduced processing temperature. Effective chain penetration and strong intermolecular interactions in conjunction with chemical crosslinking occurred between WG and the amorphous components in WF. However, the thermal decomposition of the WG component also occurred at increased temperatures, resulting in a decrease in the mechanical strength of the WF/WG composites. The result has demonstrated that ECAP is a promising methodology to produce renewable and degradable biocomposites from wood waste. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Yoo, Soohaeng; Xantheas, Sotiris S.

Water's function as a universal solvent and its role in mediating several biological functions that are responsible for sustaining life has created tremendous interest in the understanding of its structure at the molecular level.1 Due to the size of the simulation cells and the sampling time needed to compute many macroscopic properties, most of the initial simulations are performed using a classical force field whereas several processes that involve chemistry are subsequently probed with electronic structure based methods. A significant effort has therefore been devoted towards the development of classical force fields for water.2 Clusters of water molecules are usefulmore » in probing the intermolecular interactions at the microscopic level as well as providing information about the subtle energy differences that are associated with different bonding arrangements within a hydrogen bonded network. They moreover render a quantitative picture of the nature and magnitude of the various components of the intermolecular interactions such as exchange, dispersion, induction etc. They can finally serve as a vehicle for the study of the convergence of properties with increasing size.« less

Structural analysis and antimicrobial activity of 2[1H]-pyrimidinethione/selenone derivatives

NASA Astrophysics Data System (ADS)

Żesławska, Ewa; Korona-Głowniak, Izabela; Szczesio, Małgorzata; Olczak, Andrzej; Żylewska, Alicja; Tejchman, Waldemar; Malm, Anna

2017-08-01

Four new crystal structures of sulfur and selenium analogues of 2[1H]-pyrimidinone derivatives were determined with the use of X-ray diffraction method. The molecular geometry and intermolecular interactions of the investigated molecules were analyzed in order to find the structural features and geometrical parameters, which can be responsible for antimicrobial activities. The influence of chalcogen substituents (sulfur and selenium) on the crystal packing was also studied. The main differences in the molecular structures exist in mutual arrangement of two aromatic rings. The intermolecular interactions in all investigated compounds are similar. Furthermore, the in vitro antibacterial and antifungal activities for these compounds were evaluated. Preliminary investigations have identified two highly potent antibacterial compounds containing selenium atom, which display selectivity towards staphylococci and micrococci. This selectivity was not observed for a control compound used as a drug, namely vancomycin. These compounds possess also good antifungal activity. This is the first report of biological activities of 2[1H]-pyrimidineselenone derivatives.

Role of internal motions and molecular geometry on the NMR relaxation of hydrocarbons

NASA Astrophysics Data System (ADS)

Singer, P. M.; Asthagiri, D.; Chen, Z.; Valiya Parambathu, A.; Hirasaki, G. J.; Chapman, W. G.

2018-04-01

The role of internal motions and molecular geometry on 1H NMR relaxation rates in liquid-state hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for intramolecular and intermolecular 1H-1H dipole-dipole interactions. The effects of molecular geometry and internal motions on the functional form of the autocorrelation functions are studied by comparing symmetric molecules such as neopentane and benzene to corresponding straight-chain alkanes n-pentane and n-hexane, respectively. Comparison of rigid versus flexible molecules shows that internal motions cause the intramolecular and intermolecular correlation-times to get significantly shorter, and the corresponding relaxation rates to get significantly smaller, especially for longer-chain n-alkanes. Site-by-site simulations of 1H's across the chains indicate significant variations in correlation times and relaxation rates across the molecule, and comparison with measurements reveals insights into cross-relaxation effects. Furthermore, the simulations reveal new insights into the relative strength of intramolecular versus intermolecular relaxation as a function of internal motions, as a function of molecular geometry, and on a site-by-site basis across the chain.

Brooker's merocyanine: Comparison of single crystal structures

NASA Astrophysics Data System (ADS)

Hayes, Kathleen L.; Lasher, Emily M.; Choczynski, Jack M.; Crisci, Ralph R.; Wong, Calvin Y.; Dragonette, Joseph; Deschner, Joshua; Cardenas, Allan Jay P.

2018-06-01

Brooker's merocyanine and its derivatives are well-studied molecules due to their very interesting optical properties. Merocyanine dyes exhibit different colors in solution depending on the solvent's polarity, pH, aggregation and intermolecular interactions. The synthesis of 1-methyl-4-[(oxocyclohexadienylidene)ethylidene]-1,4-dihydropyridine (MOED) dye yielded a particularly interesting solid state structure where in one crystal lattice, MOED and its protonated form are bound by hydrogen bonding interactions.

Understanding and modulating opalescence and viscosity in a monoclonal antibody formulation

PubMed Central

Salinas, Branden A; Sathish, Hasige A; Bishop, Steven M; Harn, Nick; Carpenter, John F; Randolph, Theodore W

2014-01-01

Opalescence and high viscosities can pose challenges for high concentration formulation of antibodies. Both phenomena result from protein-protein intermolecular interactions that can be modulated with solution ionic strength. We studied a therapeutic monoclonal antibody that exhibits high viscosity in solutions at low ionic strength (~20 centipoise (cP) at 90 mg/mL and 23°C) and significant opalescence at isotonic ionic strength (approximately 100 nephelometric turbidity units at 90 mg/mL and 23°C). The intermolecular interactions responsible for these effects were characterized using membrane osmometry, static light scattering and zeta potential measurements. The net protein-protein interactions were repulsive at low ionic strength (~4 mM) and attractive at isotonic ionic strengths. The high viscosities are attributed to electroviscous forces at low ionic strength and the significant opalescence at isotonic ionic strength is correlated with attractive antibody interactions. Furthermore there appears to be a connection to critical phenomena and it is suggested that the extent of opalescence is dependent on the proximity to the critical point. We demonstrate that by balancing the repulsive and attractive forces via intermediate ionic strengths and by increasing the mAb concentration above the apparent critical concentration both opalescence and viscosity can be simultaneously minimized. PMID:19475558

The experimental charge-density approach in the evaluation of intermolecular interactions. Application of a new module of the XD programming package to several solids including a pentapeptide.

PubMed

Abramov, Y A; Volkov, A; Wu, G; Coppens, P

2000-11-01

A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, L-asparagine monohydrate and the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol). The electrostatic interactions are evaluated with the atom-centered distributed multipoles from KRMM (kappa'-restricted multipole model) refinements, using the Buckingham expression for non-overlapping charge densities. Results for p-nitroaniline are compared with Hartree-Fock (HF), density functional (DFT) and Moller-Plesset (MP2) supermolecular calculations and with HF and DFT periodic calculations. The HF and DFT methods fail to predict the stability of the p-nitroaniline crystal but the results of the experimental charge-density approach (ECDA) are in good agreement with both MP2 interaction energies and the experimental lattice energy. ECDA results for L-asparagine monohydrate compare well with those from DFT supermolecular and periodic HF calculations. The disorder of the terminal group in the pentapeptide, which persists at the experimental temperature of 20 K, corresponds to an energy difference of only 0.35 kJ mol(-1), which is too small to be reproduced with current methods.

Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases.

PubMed

Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

2015-04-15

Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases. Copyright © 2015 Elsevier B.V. All rights reserved.

Physisorption of three amine terminated molecules (TMBDA, BDA, TFBDA) on the Au(111) Surface: The Role of van der Waals Interaction

NASA Astrophysics Data System (ADS)

Aminpour, Maral; Le, Duy; Rahman, Talat S.

2012-02-01

Recently, the electronic properties and alignment of tetramethyl-1,4-benzenediamine (TMBDA), 1,4-benzenediamine (BDA) and tetrafluro-1,4-benzenediamine (TFBDA) molecules were studied experimentally. Discrepancies were found for both the binding energy and the molecule tilt angle with respect to the surface, when results were compared with density functional theory calculations [1]. We have included the effect of vdW interactions both between the molecules and the Au(111) surface and find binding energies which are in very good agreement with experiments. We also find that at low coverages each of these molecules would adsorb almost parallel to the surface. N-Au bond lengths and charge redistribution on adsorption of the molecules are also analyzed. Our calculations are based on DFT using vdW-DF exchange correlation functionals. For BDA (since we are aware of experimental data), we show that for higher coverage, inclusion of intermolecular van der Waals interaction leads to tilting of the molecules with respect to the surface and formation of line structures. Our results demonstrate the central role played by intermolecular interaction in pattern formation on this surface.[4pt] [1] M. Dell'Angela et al, Nano Lett. 2010, 10, 2470; M. Kamenetska et al, J. Phys. Chem. C, 2011, 115, 12625

Imaging molecular interaction of NO on Cu(110) with a scanning tunneling microscope.

PubMed

Okuyama, Hiroshi

2014-10-01

Molecular interaction on metal surfaces is one of the central issues of surface science for the microscopic understanding of heterogeneous catalysis. In this Personal Account, I review the recent studies on NO/Cu(110) employing a scanning tunneling microscope (STM) to probe and control the molecule-molecule interaction on the surface. An individual NO molecule was observed as a characteristic dumbbell-shaped protrusion, visualizing the 2π* orbital. By manipulating the intermolecular distance with the STM, the overlap of the 2π* orbital between two NO molecules was controlled. The interaction causes the formation of the bonding and antibonding orbitals below and above the Fermi level, respectively, as a function of the intermolecular distance. The 2π* orbital also plays a role in the reaction of NO with water molecules. A water molecule donates a H-bond to NO, giving rise to the down-shift of the 2π* level below the Fermi level. This causes electron transfer from the substrate to NO, weakening, and eventually rupturing, the N-O bond. The facile bond cleavage by water molecules has implications for the catalytic reduction of NO under ambient conditions. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

MOLSIM: A modular molecular simulation software

PubMed Central

Jurij, Reščič

2015-01-01

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25994597

Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic.

PubMed

Chaudhari, Mangesh I; Holleran, Sinead A; Ashbaugh, Henry S; Pratt, Lawrence R

2013-12-17

The osmotic second virial coefficients, B2, for atomic-sized hard spheres in water are attractive (B2 < 0) and become more attractive with increasing temperature (ΔB2/ΔT < 0) in the temperature range 300 K ≤ T ≤ 360 K. Thus, these hydrophobic interactions are attractive and endothermic at moderate temperatures. Hydrophobic interactions between atomic-sized hard spheres in water are more attractive than predicted by the available statistical mechanical theory. These results constitute an initial step toward detailed molecular theory of additional intermolecular interaction features, specifically, attractive interactions associated with hydrophobic solutes.

Highly viscous antibody solutions are a consequence of network formation caused by domain-domain electrostatic complementarities: insights from coarse-grained simulations.

PubMed

Buck, Patrick M; Chaudhri, Anuj; Kumar, Sandeep; Singh, Satish K

2015-01-05

Therapeutic monoclonal antibody (mAb) candidates that form highly viscous solutions at concentrations above 100 mg/mL can lead to challenges in bioprocessing, formulation development, and subcutaneous drug delivery. Earlier studies of mAbs with concentration-dependent high viscosity have indicated that mAbs with negatively charged Fv regions have a dipole-like quality that increases the likelihood of reversible self-association. This suggests that weak electrostatic intermolecular interactions can form transient antibody networks that participate in resistance to solution deformation under shear stress. Here this hypothesis is explored by parametrizing a coarse-grained (CG) model of an antibody using the domain charges from four different mAbs that have had their concentration-dependent viscosity behaviors previously determined. Multicopy molecular dynamics simulations were performed for these four CG mAbs at several concentrations to understand the effect of surface charge on mass diffusivity, pairwise interactions, and electrostatic network formation. Diffusion coefficients computed from simulations were in qualitative agreement with experimentally determined viscosities for all four mAbs. Contact analysis revealed an overall greater number of pairwise interactions for the two mAbs in this study with high concentration viscosity issues. Further, using equilibrated solution trajectories, the two mAbs with high concentration viscosity issues quantitatively formed more features of an electrostatic network than the other mAbs. The change in the number of these network features as a function of concentration is related to the number of pairwise interactions formed by electrostatic complementarities between antibody domains. Thus, transient antibody network formation caused by domain-domain electrostatic complementarities is the most probable origin of high concentration viscosity for mAbs in this study.

A series of Ln-p-chlorobenzoic acid–terpyridine complexes: lanthanide contraction effects, supramolecular interactions and luminescent behavior

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

Carter, Korey P.; Pope, Simon J. A.; Cahill, Christopher L.

Fifteen new lanthanide p-chlorobenzoic acid complexes, [PrL3(terpy)(H2O)]2 (1), [LnL3(terpy)(H2O)]2 (Ln = Nd (2), Sm (3), and Eu (4)), and [LnL3(terpy)(H2O)] (Ln = Sm (3'), Eu (4'), Gd (5), Tb (6), Dy (7), Ho (8), Er (9), Tm (10), Yb (11), Lu (12), and Y (13); HL: p-chlorobenzoic acid; terpy: 2,2':6',2''-terpyridine), have been synthesized hydrothermally at varying temperatures and structurally characterized by single crystal and powder X-ray diffraction. The series is comprised of binuclear molecular units (Pr–Eu) that give way to mononuclear molecular complexes (Sm–Y) as the lanthanide contraction takes effect. All fifteen complexes feature a tridentate terpyridine ligand, p-chlorobenzoic acidmore » ligands exhibiting multiple binding modes, bidentate, bridging bidentate, and monodentate, and a bound water molecule. Binuclear complexes 1–4 are stitched together via intermolecular interactions: aromatic–aromatic interactions for 1, halogen•••halogen interactions for 2–4, to form 1D chains. Mononuclear complexes 3', 4', and 5–13 utilize supramolecular hydrogen and halogen bonding to form 2D sheets. Visible and near-IR solid state luminescence studies were performed on complexes 2, 3, 3', 4, 4', 6, 7 and 11 and the characteristic visible luminescence of Sm(III), Eu(III), Tb(III), and Dy(III) was exhibited. The near-IR spectra of the Nd(III) and Yb(III) complexes exhibit weak characteristic luminescence, showing that terpy can act as a sensitizing chromophore in these systems.« less

μ-Carbonato-bis-(bis-{2-[(diethyl-amino)-meth-yl]phen-yl}bis-muth(III)).

PubMed

Soran, Albert P; Nema, Mihai G; Breunig, Hans J; Silvestru, Cristian

2011-01-12

The mol-ecular structure of the title compound, [Bi(2)(C(11)H(16)N)(4)(CO(3))], consists of a symmetrically bridging carbonato group which binds two [2-Et(2)NCH(2)C(6)H(4)](2)Bi units that are crystallographically related via a twofold rotation axis bis-ecting the carbonate group. The two Bi atoms and two of the C atoms directly bonded to bis-muth are quasi-planar [deviations of 0.323 (1) and 0.330 (9)Å for the Bi and C atoms, respectively] with the carbonate group. The remaining two ligands are in a trans arrangement relative to the quasi-planar (CBi)(2)CO(3) system. The metal atom is strongly coordinated by the N atom of one pendant arm [Bi-N = 2.739 (6) Å], almost trans to the O atom, while the N atom of the other pendant arm exhibits a weaker intra-molecular inter-action [Bi⋯N = 3.659 (7) Å] almost trans to a C atom. If both these intra-molecular N→Bi inter-actions per metal atom are considered, the overall coordination geometry at bis-muth becomes distorted square-pyramidal [(C,N)(2)BiO cores] and the compound can be described as a hypervalent 12-Bi-5 species. Additional quite short intra-molecular Bi⋯O inter-actions are also present [3.796 (8)-4.020 (9) Å]. Inter-molecular associations through weak η(6)⋯Bi inter-actions [Bi⋯centroid of benzene ring = 3.659 (1) Å] lead to a ribbon-like supra-molecular association.

The application of midbond basis sets in efficient and accurate ab initio calculations on electron-deficient systems

NASA Astrophysics Data System (ADS)

Choi, Chu Hwan

2002-09-01

Ab initio chemistry has shown great promise in reproducing experimental results and in its predictive power. The many complicated computational models and methods seem impenetrable to an inexperienced scientist, and the reliability of the results is not easily interpreted. The application of midbond orbitals is used to determine a general method for use in calculating weak intermolecular interactions, especially those involving electron-deficient systems. Using the criteria of consistency, flexibility, accuracy and efficiency we propose a supermolecular method of calculation using the full counterpoise (CP) method of Boys and Bernardi, coupled with Moller-Plesset (MP) perturbation theory as an efficient electron-correlative method. We also advocate the use of the highly efficient and reliable correlation-consistent polarized valence basis sets of Dunning. To these basis sets, we add a general set of midbond orbitals and demonstrate greatly enhanced efficiency in the calculation. The H2-H2 dimer is taken as a benchmark test case for our method, and details of the computation are elaborated. Our method reproduces with great accuracy the dissociation energies of other previous theoretical studies. The added efficiency of extending the basis sets with conventional means is compared with the performance of our midbond-extended basis sets. The improvement found with midbond functions is notably superior in every case tested. Finally, a novel application of midbond functions to the BH5 complex is presented. The system is an unusual van der Waals complex. The interaction potential curves are presented for several standard basis sets and midbond-enhanced basis sets, as well as for two popular, alternative correlation methods. We report that MP theory appears to be superior to coupled-cluster (CC) in speed, while it is more stable than B3LYP, a widely-used density functional theory (DFT). Application of our general method yields excellent results for the midbond basis sets. Again they prove superior to conventional extended basis sets. Based on these results, we recommend our general approach as a highly efficient, accurate method for calculating weakly interacting systems.

Design and Conformational Analysis of Peptoids Containing N-Hydroxy Amides Reveals a Unique Sheet-Like Secondary Structure

PubMed Central

Crapster, J. Aaron; Stringer, Joseph R.; Guzei, Ilia A.; Blackwell, Helen E.

2011-01-01

N-hydroxy amides can be found in many naturally occurring and synthetic compounds and are known to act as both strong proton donors and chelators of metal cations. We have initiated studies of peptoids, or N-substituted glycines, that contain N-hydroxy amide side chains to investigate the potential effects of these functional groups on peptoid backbone amide rotamer equilibria and local conformations. We reasoned that the propensity of these functional groups to participate in hydrogen bonding could be exploited to enforce intramolecular or intermolecular interactions that yield new peptoid structures. Here, we report the design, synthesis, and detailed conformational analysis of a series of model N-hydroxy peptoids. These peptoids were readily synthesized, and their structures were analyzed in solution by 1D and 2D NMR and in the solid-state by X-ray crystallography. The N-hydroxy amides were found to strongly favor trans conformations with respect to the peptoid backbone in chloroform. More notably, unique sheet-like structures held together via intermolecular hydrogen bonds were observed in the X-ray crystal structures of an N-hydroxy amide peptoid dimer, which to our knowledge represent the first structure of this type reported for peptoids. These results suggest that the N-hydroxy amide can be utilized to control both local backbone geometries and longer-range intermolecular interactions in peptoids, and represents a new functional group in the peptoid design toolbox. PMID:22180908

Nuclear spin relaxation in ligands outside of the first coordination sphere in a gadolinium (III) complex: Effects of intermolecular forces

NASA Astrophysics Data System (ADS)

Kruk, Danuta; Kowalewski, Jozef

2002-07-01

This article describes paramagnetic relaxation enhancement (PRE) in systems with high electron spin, S, where there is molecular interaction between a paramagnetic ion and a ligand outside of the first coordination sphere. The new feature of our treatment is an improved handling of the electron-spin relaxation, making use of the Redfield theory. Following a common approach, a well-defined second coordination sphere is assumed, and the PRE contribution from these more distant and shorter-lived ligands is treated in a way similar to that used for the first coordination sphere. This model is called "ordered second sphere," OSS. In addition, we develop here a formalism similar to that of Hwang and Freed [J. Chem. Phys. 63, 4017 (1975)], but accounting for the electron-spin relaxation effects. We denote this formalism "diffuse second sphere," DSS. The description of the dynamics of the intermolecular dipole-dipole interaction is based on the Smoluchowski equation, with a potential of mean force related to the radial distribution function. We have used a finite-difference method to calculate numerically a correlation function for translational motion, taking into account the intermolecular forces leading to an arbitrary radial distribution of the ligand protons. The OSS and DSS models, including the Redfield description of the electron-spin relaxation, were used to interpret the PRE in an aqueous solution of a slowly rotating gadolinium (III) complex (S=7/2) bound to a protein.

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

NASA Astrophysics Data System (ADS)

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

2006-08-01

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

How Structure Defines Affinity in Protein-Protein Interactions

PubMed Central

Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

2014-01-01

Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

Development of Monopole Interaction Models for Ionic Compounds. Part I: Estimation of Aqueous Henry's Law Constants for Ions and Gas Phase pKa Values for Acidic Compounds.

PubMed

Hilal, S H; Saravanaraj, A N; Carreira, L A

2014-02-01

The SPARC (SPARC Performs Automated Reasoning in Chemistry) physicochemical mechanistic models for neutral compounds have been extended to estimate Henry's Law Constant (HLC) for charged species by incorporating ionic electrostatic interaction models. Combinations of absolute aqueous pKa values, relative pKa values in the gas phase, and aqueous HLC for neutral compounds have been used to develop monopole interaction models that quantify the energy differences upon moving an ionic solute molecule from the gas phase to the liquid phase. Inter-molecular interaction energies were factored into mechanistic contributions of monopoles with polarizability, dipole, H-bonding, and resonance. The monopole ionic models were validated by a wide range of measured gas phase pKa data for 450 acidic compounds. The RMS deviation error and R(2) for the OH, SH, CO2 H, CH3 and NR2 acidic reaction centers (C) were 16.9 kcal/mol and 0.87, respectively. The calculated HLCs of ions were compared to the HLCs of 142 ions calculated by quantum mechanics. Effects of inter-molecular interaction of the monopoles with polarizability, dipole, H-bonding, and resonance on acidity of the solutes in the gas phase are discussed. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermolecular interaction of fosinopril with bovine serum albumin (BSA): The multi-spectroscopic and computational investigation.

PubMed

Zhou, Kai-Li; Pan, Dong-Qi; Lou, Yan-Yue; Shi, Jie-Hua

2018-04-16

The intermolecular interaction of fosinopril, an angiotensin converting enzyme inhibitor with bovine serum albumin (BSA), has been investigated in physiological buffer (pH 7.4) by multi-spectroscopic methods and molecular docking technique. The results obtained from fluorescence and UV absorption spectroscopy revealed that the fluorescence quenching mechanism of BSA induced by fosinopril was mediated by the combined dynamic and static quenching, and the static quenching was dominant in this system. The binding constant, K b , value was found to lie between 2.69 × 10 3 and 9.55 × 10 3  M -1 at experimental temperatures (293, 298, 303, and 308 K), implying the low or intermediate binding affinity between fosinopril and BSA. Competitive binding experiments with site markers (phenylbutazone and diazepam) suggested that fosinopril preferentially bound to the site I in sub-domain IIA on BSA, as evidenced by molecular docking analysis. The negative sign for enthalpy change (ΔH 0 ) and entropy change (ΔS 0 ) indicated that van der Waals force and hydrogen bonds played important roles in the fosinopril-BSA interaction, and 8-anilino-1-naphthalenesulfonate binding assay experiments offered evidence of the involvements of hydrophobic interactions. Moreover, spectroscopic results (synchronous fluorescence, 3-dimensional fluorescence, and Fourier transform infrared spectroscopy) indicated a slight conformational change in BSA upon fosinopril interaction. Copyright © 2018 John Wiley & Sons, Ltd.

Universal scaling of potential energy functions describing intermolecular interactions. II. The halide-water and alkali metal-water interactions

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

Werhahn, Jasper C.; Akase, Dai; Xantheas, Sotiris S.

2014-08-14

The scaled versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys.141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions – Mie, Lennard-Jones, Morse, and Buckingham exponential-6 – have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X -(H 2O), X = F, Cl, Br, I, and alkali metal-water, M +(H 2O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits tomore » the ab initio data that are between one and two orders of magnitude better in the χ 2 than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. Finally, the fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.« less

On the influence of the intermolecular potential on the wetting properties of water on silica surfaces

NASA Astrophysics Data System (ADS)

Pafong, E.; Geske, J.; Drossel, B.

2016-09-01

We study the wetting properties of water on silica surfaces using molecular dynamics (MD) simulations. To describe the intermolecular interaction between water and silica atoms, two types of interaction potential models are used: the standard BródkA and Zerda (BZ) model and the Gulmen and Thompson (GT) model. We perform an in-depth analysis of the influence of the choice of the potential on the arrangement of the water molecules in partially filled pores and on top of silica slabs. We find that at moderate pore filling ratios, the GT silica surface is completely wetted by water molecules, which agrees well with experimental findings, while the commonly used BZ surface is less hydrophilic and is only partially wetted. We interpret our simulation results using an analytical calculation of the phase diagram of water in partially filled pores. Moreover, an evaluation of the contact angle of the water droplet on top of the silica slab reveals that the interaction becomes more hydrophilic with increasing slab thickness and saturates around 2.5-3 nm, in agreement with the experimentally found value. Our analysis also shows that the hydroaffinity of the surface is mainly determined by the electrostatic interaction, but the van der Waals interaction nevertheless is strong enough that it can turn a hydrophobic surface into a hydrophilic surface.

New copper complexes with bipyrazolic ligands: Synthesis, characterization and evaluation of the antibacterial and catalytic properties

NASA Astrophysics Data System (ADS)

Harit, Tarik; Abouloifa, Houssam; Tillard, Monique; Eddike, Driss; Asehraou, Abdeslam; Malek, Fouad

2018-07-01

The synthesis of new bipyrazolic ligands functionalized by carboxyl groups, namely 3-Bis(3‧-carboxyl-5‧-methyl-l'-pyrazolyl) propan-2-ol (L1) and 1,3-Bis(3‧-carboxyl-5‧-methyl-l '-pyrazolyl),2-methyl propane (L2) is reported. Their corresponding [C13H15CuN4O5] (CuL1) and [C14H16CuN4O4] (CuL2) copper (II) complexes are also elaborated and characterized by elemental analysis, FTIR an UV-visible spectroscopy. The crystal structure of the CuL1 complex confirms that copper atom is 4-coordinated, in a distorted square planar geometry within the molecule, and achieves its coordination through weak intermolecular interactions leading to two dimensional slabs. This geometry is in agreement with UV-visible results which also evidence that structure of complexes are affected in DMSO in contrast to methanol. No antibacterial activity against all the tested bacterial strains has been found for the Cu (II) complexes. By contrast, CuL1 is characterized with good catalytic properties in the air-oxidation of catechol substrate to quinone.

Controlled synthesis of organic single-crystalline nanowires via the synergy approach of the bottom-up/top-down processes.

PubMed

Zhuo, Ming-Peng; Zhang, Ye-Xin; Li, Zhi-Zhou; Shi, Ying-Li; Wang, Xue-Dong; Liao, Liang-Sheng

2018-03-15

The controlled fabrication of organic single-crystalline nanowires (OSCNWs) with a uniform diameter in the nanoscale via the bottom-up approach, which is just based on weak intermolecular interaction, is a great challenge. Herein, we utilize the synergy approach of the bottom-up and the top-down processes to fabricate OSCNWs with diameters of 120 ± 10 nm through stepwise evolution processes. Specifically, the evolution processes vary from the self-assembled organic micro-rods with a quadrangular pyramid-like end-structure bounded with {111}s and {11-1}s crystal planes to the "top-down" synthesized organic micro-rods with the flat cross-sectional {002}s plane, to the organic micro-tubes with a wall thickness of ∼115 nm, and finally to the organic nanowires. Notably, the anisotropic etching process caused by the protic solvent molecules (such as ethanol) is crucial for the evolution of the morphology throughout the whole top-down process. Therefore, our demonstration opens a new avenue for the controlled-fabrication of organic nanowires, and also contributes to the development of nanowire-based organic optoelectronics such as organic nanowire lasers.

5Beta,6beta-epoxy-17-oxoandrostan-3beta-yl acetate and 5beta,6beta-epoxy-20-oxopregnan-3beta-yl acetate.

PubMed

Pinto, Rui M A; Salvador, Jorge A R; Paixão, José A

2008-05-01

In the title compounds, C(21)H(30)O(4), (I), and C(23)H(34)O(4), (II), respectively, which are valuable intermediates in the synthesis of important steroid derivatives, rings A and B are cis-(5beta,10beta)-fused. The two molecules have similar conformations of rings A, B and C. The presence of the 5beta,6beta-epoxide group induces a significant twist of the steroid nucleus and a strong flattening of the B ring. The different C17 substituents result in different conformations for ring D. Cohesion of the molecular packing is achieved in both compounds only by weak intermolecular interactions. The geometries of the molecules in the crystalline environment are compared with those of the free molecules as given by ab initio Roothan Hartree-Fock calculations. We show in this work that quantum mechanical ab initio methods reproduce well the details of the conformation of these molecules, including a large twist of the steroid nucleus. The calculated twist values are comparable, but are larger than the observed values, indicating a possible small effect of the crystal packing on the twist angles.

Structural and microstructural description of the glacial state in triphenyl phosphite from powder synchrotron X-ray diffraction data and Raman scattering investigations

NASA Astrophysics Data System (ADS)

Derollez, P.; Hernandez, O.; Hédoux, A.; Guinet, Y.; Masson, O.; Lefebvre, J.; Descamps, M.

2004-06-01

The structure and microstructure (refinement of the isotropic size and microstrain parameters) of the glacial state in triphenyl phosphite (TPP, P(OC 6H 5) 3) transformed at 222K have been determined from powder synchrotron X-ray diffraction data through a Rietveld and a Le Bail refinement, respectively. It is shown that the glacial state is composed of crystallites of the stable crystal phase coexisting with non-transformed supercooled liquid, the apparent size of the crystallites—depending on the aging temperature at which the glacial state is isothermally formed, [Phys. Rev. B 60 (1999) 9390]—being equal to 329.2(2) Å at 222K. The molecular conformation is slightly less mirror-symmetric than the one in the crystal state, and correlatively only one of the two unusual weak intermolecular C-H⋯O hydrogen bonds already observed in the latter state is encountered in the glacial one. Additional Raman scattering investigations confirm the previous result and reveal in addition that no hydrogen bonding interaction is observed neither in the glass nor in the liquid states.

Thermolysis synthesis of pure phase NiO from novel sonochemical synthesized Ni(II) nano metal-organic supramolecular architecture.

PubMed

Hanifehpour, Younes; Morsali, Ali; Mirtamizdoust, Babak; Joo, Sang Woo; Soltani, Behzad

2017-07-01

Nano-structures of a new supramolecular coordination compound of divalent nickel with the pyrazol (pzH) containing the terminal azide anions, [Ni(pzH) 2 (N 3 ) 2 ] (1), with discrete molecular architecture (DMA) in solid state was synthesized via sonochemical method. The new nanostructure was characterized by scanning electron microscopy, X-ray powder diffraction, IR, and elemental analysis. Compound 1 was structurally characterized by single crystal X-ray diffraction and the single-crystal X-ray data shows that the coordination number of Ni (II) ions is six, (NiN 6 ), with four N-donor atoms from neutral "pzH" ligands and two N-donors from two terminal azide anions. The supramolecular features in these complexes are guided and controlled by weak directional intermolecular interactions. The structure of the title complex was optimized by density functional theory calculations. Calculated structural parameters and IR spectra for the title complex are consistent with the crystal structure. The NiO nanoparticles were obtained by thermolysis of 1 at 180°C with oleic acid as a surfactant. Copyright © 2017 Elsevier B.V. All rights reserved.

Charge transfer in the weak driving force limit in blends of MDMO-PPV and dithienylthiazolo[5,4-d]thiazoles towards organic photovoltaics with high V(OC).

PubMed

Nevil, Nissy; Ling, Yun; Van Mierloo, Sarah; Kesters, Jurgen; Piersimoni, Fortunato; Adriaensens, Peter; Lutsen, Laurence; Vanderzande, Dirk; Manca, Jean; Maes, Wouter; Van Doorslaer, Sabine; Goovaerts, Etienne

2012-12-05

A series of three 5'-aryl-2,5-dithienylthiazolo[5,4-d]thiazole (DTTzTz) semiconducting molecules with different aryl substituents has been investigated as alternative acceptor materials in combination with the donor polymer poly[2-methoxy-5-(3',7'-dimethyloctyloxy)-1,4-phenylene vinylene] (MDMO-PPV) in order to evaluate the photoinduced charge transfer (CT) efficiency in the resulting blends, designed towards possible application in organic photovoltaics. Photoluminescence quenching together with polaron detection by electron paramagnetic resonance and photoinduced absorption (PIA) demonstrate an increasing charge transfer efficiency when the DTTzTz substituents are varied from thien-2-yl to 4-trifluoromethylphenyl and 4-cyanophenyl groups, correlating well with the increasing acceptor strength in this series of molecules. In line with this observation, there is a decrease in the effective optical bandgap relative to pure MDMO-PPV that becomes more pronounced along this series of acceptor compounds, reaching 0.12 eV in the blend with 4-CN-Ph-DTTzTz. Intermolecular interactions between the blend components lead to lower energy transitions which are found to contribute significantly to the device external quantum efficiency. The high V(OC) reached in devices based on MDMO-PPV:4-CN-Ph-DTTzTz blends meets the expectations for such a donor:acceptor combination. However, thermal activation of charge carrier recombination occurs because of the weak driving force for charge transfer, as shown by time-dependent PIA measurements, and this is suggested as a cause for the observed low photovoltaic performance.

ELUTION OF ORGANIC SOLUTES FROM DIFFERENT POLARITY SORBENTS USING SUBCRITICAL WATER. (R825394)

EPA Science Inventory

The intermolecular interactions between organic solutes and sorbent matrices under subcritical water conditions have been investigated at a pressure of 50 bar and temperatures ranging from 50 to 250°C. Both polar and nonpolar organics (chlorophenols, amines, n-alkanes...

Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD

NASA Astrophysics Data System (ADS)

Blanco-Díaz, Edgar G.; Vázquez-Montelongo, Erik A.; Cisneros, G. Andrés; Castrejón-González, Edgar Omar

2018-02-01

Non-covalent interactions (NCIs) play a crucial role in the behavior and properties of ionic liquids (ILs). These interactions are particularly important for non-equilibrium properties such as the change in viscosity due to shearing forces (shear viscosity). Therefore, a detailed understanding of these interactions can improve our understanding of these important classes of liquids. Here, we have employed quantum mechanical energy decomposition analysis (EDA) and NCI analysis to investigate a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. EDA based on symmetry-adapted perturbation theory (SAPT) for the complete monomers, as well as fragment SAPT (FSAPT), for the functional fragments has been carried out. In general, the electrostatic component comprises ≈80% of the intermolecular interaction, and significant contributions from other components (induction and dispersion) are also observed, especially for interactions involving bifurcated hydrogen bonds. The FSAPT analysis suggests that caution is warranted when employing simplified assumptions for non-bonded interactions, e.g., focusing only on hydrogen bonds between functional fragments, since this view may not provide a complete picture of the complicated interactions between the ions. In non-equilibrium molecular dynamics, the total interaction energies of some fragments have a significant qualitative change as the shear rate increases. Our results indicate that the inter-fragment interactions play a fundamental role in the viscous behavior of ILs, suggesting that the exclusive use of geometric criteria to analyze inter-molecular interactions in these systems is not sufficient to investigate shear-thinning effects.

Direct measurements of intermolecular forces by chemical force microscopy

NASA Astrophysics Data System (ADS)

Vezenov, Dmitri Vitalievich

1999-12-01

Detailed description of intermolecular forces is key to understanding a wide range of phenomena from molecular recognition to materials failure. The unique features of atomic force microscopy (AFM) to make point contact force measurements with ultra high sensitivity and to generate spatial maps of surface topography and forces have been extended to include measurements between well-defined organic molecular groups. Chemical modification of AFM probes with self-assembled monolayers (SAMs) was used to make them sensitive to specific molecular interactions. This novel chemical force microscopy (CFM) technique was used to probe forces between different molecular groups in a range of environments (vacuum, organic liquids and aqueous solutions); measure surface energetics on a nanometer scale; determine pK values of the surface acid and base groups; measure forces to stretch and unbind a short synthetic DNA duplex and map the spatial distribution of specific functional groups and their ionization state. Studies of adhesion forces demonstrated the important contribution of hydrogen bonding to interactions between simple organic functionalities. The chemical identity of the tip and substrate surfaces as well as the medium had a dramatic effect on adhesion between model monolayers. A direct correlation between surface free energy and adhesion forces was established. The adhesion between epoxy polymer and model mixed SAMs varied with the amount of hydrogen bonding component in the monolayers. A consistent interpretation of CFM measurements in polar solvents was provided by contact mechanics models and intermolecular force components theory. Forces between tips and surfaces functionalized with SAMs terminating in acid or base groups depended on their ionization state. A novel method of force titration was introduced for highly local characterization of the pK's of surface functional groups. The pH-dependent changes in friction forces were exploited to map spatially the changes in ionization state on SAM surfaces. The phase contrast in tapping mode AFM between chemically distinct monolayer regions and corresponding adhesion forces were found to be directly correlated. Thus, both friction and intermittent contact CFM images could be interpreted in terms of the strength of intermolecular interactions. CFM was also used to probe biomolecular interactions. Separation forces between complementary oligonucleotide strands were significantly larger than the forces measured between noncomplementary strands and were consistent with the unbinding of a single DNA duplex. CFM data provided a direct measure of the forces required to elastically deform, structurally-transform and separate well-defined, synthetic duplexes into single strand oligonucleotides.

Structure and Thermodynamics of Polyolefin Melts

NASA Astrophysics Data System (ADS)

Weinhold, J. D.; Curro, J. G.; Habenschuss, A.; Londono, J. D.

1997-03-01

Subtle differences in the intermolecular packing of various polyolefins can create dissimilar permeability and mixing behavior. We have used a combination of the Polymer Reference Interaction Site Model (PRISM) and Monte Carlo simulation to study the structural and thermodynamic properties of realistic models for polyolefins. Results for polyisobutylene and syndiotactic polypropylene will be presented along with comparisons to wide-angle x-ray scattering experiments and properties determined from previous studies of polyethylene and isotactic polypropylene. Our technique uses a Monte Carlo simulation on an isolated molecule to determine the polymer's intramolecular structure. With this information, PRISM theory can predict the intermolecular packing for any liquid density and/or mixture composition in a computationally efficient manner. This approach will then be used to explore the mixing behavior of these polyolefins.

Intramolecular and intermolecular vibrational energy relaxation of CH 2I 2 dissolved in supercritical fluid

NASA Astrophysics Data System (ADS)

Sekiguchi, K.; Shimojima, A.; Kajimoto, O.

2002-04-01

A pump-probe experiment was performed to examine vibrational population relaxation of diiodomethane (CH 2I 2) molecule dissolved in supercritical CO 2. Using an apparatus with femtosecond time resolution, we observed the contributions of intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) separately. IVR and VET rates were measured with varying solvent densities at a constant temperature. It is shown that the IVR rate is not density dependent while the VET rate increases with increasing density from 0.4 to 0.8 g cm-3. This observation suggests that the rate of the VET process is determined by solute-solvent collisions whereas the IVR rate is not much affected by solute-solvent interaction.

Influence of pressure on the crystallization of systems characterized by different intermolecular attraction

NASA Astrophysics Data System (ADS)

Koperwas, K.; Affouard, F.; Gerges, J.; Valdes, L.-C.; Adrjanowicz, K.; Paluch, M.

2017-12-01

In this paper, we examine, in terms of the classical nucleation theory, how the strengthening of the attractive intermolecular interactions influences the crystallization process for systems like Lennard-Jones at different isobaric conditions. For this purpose, we modify the standard Lennard-Jones potential, and as a result, we obtain three different systems characterized by various strengths of attractive potentials occurring between molecules, which are in direct relationship to the physical quantities describing molecules, e.g., its polarizability or dipole moment. Based on performed analysis, we demonstrate that the molecular attraction primarily impacts the thermodynamics of the interface between liquid and crystal. This is reflected in the behavior of nucleation and overall crystallization rates during compression of the system.

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study.

PubMed

Altun, Ahmet; Neese, Frank; Bistoni, Giovanni

2018-01-01

The local energy decomposition (LED) analysis allows for a decomposition of the accurate domain-based local pair natural orbital CCSD(T) [DLPNO-CCSD(T)] energy into physically meaningful contributions including geometric and electronic preparation, electrostatic interaction, interfragment exchange, dynamic charge polarization, and London dispersion terms. Herein, this technique is employed in the study of hydrogen-bonding interactions in a series of conformers of water and hydrogen fluoride dimers. Initially, DLPNO-CCSD(T) dissociation energies for the most stable conformers are computed and compared with available experimental data. Afterwards, the decay of the LED terms with the intermolecular distance ( r ) is discussed and results are compared with the ones obtained from the popular symmetry adapted perturbation theory (SAPT). It is found that, as expected, electrostatic contributions slowly decay for increasing r and dominate the interaction energies in the long range. London dispersion contributions decay as expected, as r -6 . They significantly affect the depths of the potential wells. The interfragment exchange provides a further stabilizing contribution that decays exponentially with the intermolecular distance. This information is used to rationalize the trend of stability of various conformers of the water and hydrogen fluoride dimers.

A new 1D manganese(II) coordination polymer with end-to-end azide bridge and isonicotinoylhydrazone Schiff base ligand: Crystal structure, Hirshfeld surface, NBO and thermal analyses

NASA Astrophysics Data System (ADS)

Khani, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

2018-02-01

A new manganese (II) coordination polymer, [MnL2 (μ-1,3-N3)2]n, with co-ligands including azide anion and Schiff base based on isonicotinoylhydrazone has been synthesized and characterized. The crystal structure determination shows that the azide ligand acts as end-to-end (EE) bridging ligand and generates a one-dimensional coordination polymer. In this compound, each manganes (II) metal center is hexa-coordinated by four azide nitrogens and two pyridinic nitrogens for the formation of octahedral geometry. The analysis of crystal packing indicates that the 1D chain of [MnL2 (μ-1,3-N3)2]n, is stabilized as a 3D supramolecular network by intra- and inter-chain intermolecular interactions of X-H···Y (X = N and C, Y = O and N). Hirshfeld surface analysis and 2D fingerprint plots have been used for a more detailed investigation of intermolecular interactions. Also, natural bond orbital (NBO) analysis was performed to get information about atomic charge distributions, hybridizations and the strength of interactions. Finally, thermal analysis of compound showed its complete decomposition during three thermal steps.