atom dihedral angles: Topics by Science.gov

Sample records for atom dihedral angles

Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.

PubMed

Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

2009-12-31

To systematically construct a low-dimensional free-energy landscape of RNA systems from a classical molecular dynamics simulation, various versions of the principal component analysis (PCA) are compared: the cPCA using the Cartesian coordinates of all atoms, the dPCA using the sine/cosine-transformed six backbone dihedral angles as well as the glycosidic torsional angle chi and the pseudorotational angle P, the aPCA which ignores the circularity of the 6 + 2 dihedral angles of the RNA, and the dPCA(etatheta), which approximates the 6 backbone dihedral angles by 2 pseudotorsional angles eta and theta. As representative examples, a 10-nucleotide UUCG hairpin and the 36-nucleotide segment SL1 of the Psi site of HIV-1 are studied by classical molecular dynamics simulation, using the Amber all-atom force field and explicit solvent. It is shown that the conformational heterogeneity of the RNA hairpins can only be resolved by an angular PCA such as the dPCA but not by the cPCA using Cartesian coordinates. Apart from possible artifacts due to the coupling of overall and internal motion, this is because the details of hydrogen bonding and stacking interactions but also of global structural rearrangements of the RNA are better discriminated by dihedral angles. In line with recent experiments, it is found that the free energy landscape of RNA hairpins is quite rugged and contains various metastable conformational states which may serve as an intermediate for unfolding.
Realistic sampling of amino acid geometries for a multipolar polarizable force field

PubMed Central

Hughes, Timothy J.; Cardamone, Salvatore

2015-01-01

The Quantum Chemical Topological Force Field (QCTFF) uses the machine learning method kriging to map atomic multipole moments to the coordinates of all atoms in the molecular system. It is important that kriging operates on relevant and realistic training sets of molecular geometries. Therefore, we sampled single amino acid geometries directly from protein crystal structures stored in the Protein Databank (PDB). This sampling enhances the conformational realism (in terms of dihedral angles) of the training geometries. However, these geometries can be fraught with inaccurate bond lengths and valence angles due to artefacts of the refinement process of the X‐ray diffraction patterns, combined with experimentally invisible hydrogen atoms. This is why we developed a hybrid PDB/nonstationary normal modes (NM) sampling approach called PDB/NM. This method is superior over standard NM sampling, which captures only geometries optimized from the stationary points of single amino acids in the gas phase. Indeed, PDB/NM combines the sampling of relevant dihedral angles with chemically correct local geometries. Geometries sampled using PDB/NM were used to build kriging models for alanine and lysine, and their prediction accuracy was compared to models built from geometries sampled from three other sampling approaches. Bond length variation, as opposed to variation in dihedral angles, puts pressure on prediction accuracy, potentially lowering it. Hence, the larger coverage of dihedral angles of the PDB/NM method does not deteriorate the predictive accuracy of kriging models, compared to the NM sampling around local energetic minima used so far in the development of QCTFF. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26235784
Random close packing in protein cores

NASA Astrophysics Data System (ADS)

Gaines, Jennifer C.; Smith, W. Wendell; Regan, Lynne; O'Hern, Corey S.

2016-03-01

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ ≈0.75 , a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ ≈0.56 , which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure.
Random close packing in protein cores.

PubMed

Gaines, Jennifer C; Smith, W Wendell; Regan, Lynne; O'Hern, Corey S

2016-03-01

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ ≈ 0.75, a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ ≈ 0.56, which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure.
Cyclic coordinate descent: A robotics algorithm for protein loop closure.

PubMed

Canutescu, Adrian A; Dunbrack, Roland L

2003-05-01

In protein structure prediction, it is often the case that a protein segment must be adjusted to connect two fixed segments. This occurs during loop structure prediction in homology modeling as well as in ab initio structure prediction. Several algorithms for this purpose are based on the inverse Jacobian of the distance constraints with respect to dihedral angle degrees of freedom. These algorithms are sometimes unstable and fail to converge. We present an algorithm developed originally for inverse kinematics applications in robotics. In robotics, an end effector in the form of a robot hand must reach for an object in space by altering adjustable joint angles and arm lengths. In loop prediction, dihedral angles must be adjusted to move the C-terminal residue of a segment to superimpose on a fixed anchor residue in the protein structure. The algorithm, referred to as cyclic coordinate descent or CCD, involves adjusting one dihedral angle at a time to minimize the sum of the squared distances between three backbone atoms of the moving C-terminal anchor and the corresponding atoms in the fixed C-terminal anchor. The result is an equation in one variable for the proposed change in each dihedral. The algorithm proceeds iteratively through all of the adjustable dihedral angles from the N-terminal to the C-terminal end of the loop. CCD is suitable as a component of loop prediction methods that generate large numbers of trial structures. It succeeds in closing loops in a large test set 99.79% of the time, and fails occasionally only for short, highly extended loops. It is very fast, closing loops of length 8 in 0.037 sec on average.
Characteristic conformation of Mosher's amide elucidated using the cambridge structural database.

PubMed

Ichikawa, Akio; Ono, Hiroshi; Mikata, Yuji

2015-07-16

Conformations of the crystalline 3,3,3-trifluoro-2-methoxy-2-phenylpropanamide derivatives (MTPA amides) deposited in the Cambridge Structural Database (CSD) were examined statistically as Racid-enantiomers. The majority of dihedral angles (48/58, ca. 83%) of the amide carbonyl groups and the trifluoromethyl groups ranged from -30° to 0° with an average angle θ1 of -13°. The other conformational properties were also clarified: (1) one of the fluorine atoms was antiperiplanar (ap) to the amide carbonyl group, forming a staggered conformation; (2) the MTPA amides prepared from primary amines showed a Z form in amide moieties; (3) in the case of the MTPA amide prepared from a primary amine possessing secondary alkyl groups (i.e., Mosher-type MTPA amide), the dihedral angles between the methine groups and the carbonyl groups were syn and indicative of a moderate conformational flexibility; (4) the phenyl plane was inclined from the O-Cchiral bond of the methoxy moiety with an average dihedral angle θ2 of +21°; (5) the methyl group of the methoxy moiety was ap to the ipso-carbon atom of the phenyl group.
Dichloridobis(phenanthridine-κN)zinc(II).

PubMed

Khoshtarkib, Zeinab; Ebadi, Amin; Alizadeh, Robabeh; Ahmadi, Roya; Amani, Vahid

2009-06-06

In the mol-ecule of the title compound, [ZnCl(2)(C(13)H(9)N)(2)], the Zn(II) atom is four-coordinated in a distorted tetra-hedral configuration by two N atoms from two phenanthridine ligands and by two terminal Cl atoms. The dihedral angle between the planes of the phenanthridine ring systems is 69.92 (3)°. An intra-molecular C-H⋯Cl inter-action results in the formation of a planar five-membered ring, which is oriented at a dihedral angle of 8.32 (3)° with respect to the adjacent phenanthridine ring system. In the crystal structure, π-π contacts between the phenanthridine systems [centroid-centroid distances = 3.839 (2), 3.617 (1) and 3.682 (1) Å] may stabilize the structure. Two weak C-H⋯π inter-actions are also found.
N-(1-Allyl-1H-indazol-5-yl)-4-methyl-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Abderrafia, Hafid; Saadi, Mohamed; El Ammari, Lahcen

2013-11-30

The asymmetric unit of the title compound, C17H17N3O2S, contains two independent mol-ecules linked by an N-H⋯O hydrogen bond. The mol-ecules show different conformations. In the first mol-ecule, the fused five- and six-membered ring system is almost perpendicular to the plane through the atoms forming the allyl group, as indicated by the dihedral angle of 85.1 (4)°. The dihedral angle with the methyl-benzene-sulfonamide group is 78.8 (1)°. On the other hand, in the second mol-ecule, the dihedral angles between the indazole plane and the allyl and methyl-benzene-sulfonamide groups are 80.3 (3) and 41.5 (1)°, respectively. In the crystal, mol-ecules are further linked by N-H⋯N and C-H⋯O hydrogen bonds, forming a three-dimensional network.
Dichloridobis(phenanthridine-κN)zinc(II)

PubMed Central

Khoshtarkib, Zeinab; Ebadi, Amin; Alizadeh, Robabeh; Ahmadi, Roya; Amani, Vahid

2009-01-01

In the molecule of the title compound, [ZnCl2(C13H9N)2], the ZnII atom is four-coordinated in a distorted tetrahedral configuration by two N atoms from two phenanthridine ligands and by two terminal Cl atoms. The dihedral angle between the planes of the phenanthridine ring systems is 69.92 (3)°. An intramolecular C—H⋯Cl interaction results in the formation of a planar five-membered ring, which is oriented at a dihedral angle of 8.32 (3)° with respect to the adjacent phenanthridine ring system. In the crystal structure, π–π contacts between the phenanthridine systems [centroid–centroid distances = 3.839 (2), 3.617 (1) and 3.682 (1) Å] may stabilize the structure. Two weak C—H⋯π interactions are also found. PMID:21582680
N-(1-Allyl-1H-indazol-5-yl)-4-methylbenzenesulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Abderrafia, Hafid; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

The asymmetric unit of the title compound, C17H17N3O2S, contains two independent molecules linked by an N—H⋯O hydrogen bond. The molecules show different conformations. In the first molecule, the fused five- and six-membered ring system is almost perpendicular to the plane through the atoms forming the allyl group, as indicated by the dihedral angle of 85.1 (4)°. The dihedral angle with the methylbenzenesulfonamide group is 78.8 (1)°. On the other hand, in the second molecule, the dihedral angles between the indazole plane and the allyl and methylbenzenesulfonamide groups are 80.3 (3) and 41.5 (1)°, respectively. In the crystal, molecules are further linked by N—H⋯N and C—H⋯O hydrogen bonds, forming a three-dimensional network. PMID:24454264
3,3-Dimethyl-1-[5-(1H-1,2,4-triazol-1-ylmethyl)-1,3,4-thiadiazol-2-ylsulfanyl]butan-2-one

PubMed Central

Wei, Qing-Li; He, Fu-Jin; Li, Fang; Bi, Sai

2008-01-01

In the molecule of the title compound, C11H15N5OS2, the thiadiazole and triazole rings are not coplanar, the dihedral angle formed by their mean planes being 59.9 (2)°. The exocyclic S atom, and the methylene, carbonyl, tert-butyl and one methyl carbon form an approximately planar zigzag chain, which makes a dihedral angle of 74.6 (1)° with the thiadiazole ring. PMID:21201440
N-[5-(Diphenylphosphorylmethyl)-4-(4-fluorophenyl)-6-isopropylpyrimidin-2-yl]-N-methylmethanesulfonamide

PubMed Central

Wu, Ya-Ming

2013-01-01

In the title compound, C28H29FN3O3PS, the pyrimidine ring is oriented at a dihedral angle of 50.9 (2)° with respect to the florobenzene ring, while the two phenyl rings bonding to the same P atom are twisted with respect to each other, making a dihedral angle of 62.2 (2)°. In the crystal, molecules are linked by weak C—H⋯O and C—H⋯F hydrogen bonds into a three-dimensional supramolecular architecture. PMID:24454107
1,1'-Bis[bis-(4-meth-oxy-phen-yl)phosphan-yl]ferrocene.

PubMed

Ren, Xinfeng; Wang, Le; Li, Ya

2012-07-01

In the crystal structure of the title substituted ferrocene complex, [Fe(C₁₉H₁₈O₂P)₂], the Fe(II) atom lies on a twofold rotation axis, giving an eclipsed cyclo-penta-dienyl conformation with a ring centroid separation of 3.292 (7) Å and an Fe-C bond-length range of 2.0239 (15)-2.0521 (15) Å. In the ligand, the cyclo-penta-dienyl ring forms dihedral angles of 60.36 (6) and 82.93 (6)° with the two benzene rings of the diphenyl-phosphine group, while the dihedral angle between the benzene rings is 67.4 (5)°.
Complexation and Structure Elucidation of the Axial Conformers of Mono- and (±)-trans-1,2-Disubstituted Cyclohexanes by Enantiopure Alleno-Acetylenic Cage Receptors.

PubMed

Gropp, Cornelius; Trapp, Nils

2018-04-25

Single crystal X-ray diffraction is a powerful method to unambiguously characterize the structure of molecules with atomic resolution. Herein, we review the molecular recognition of the (di)axial conformers of Mono- and (±)-trans-1,2-disubstituted cyclohexanes by enantiopure alleno-acetylenic cage receptors in solution and in the solid state. Single crystals of the host-guest complexes suitable for X-ray diffraction allow for the first time to study the dihedral angles of a series of Mono- and (±)-trans-1,2-disubstituted cyclohexanes in their (di)axial chair conformation. Theoretical studies indicate negligible influence of the host structure on the guest conformation, suggesting that the structural information obtained from the host-guest complexes give insight into the innate structures of Mono- and (±)-trans-1,2-disubstituted cyclohexanes. Strong deviation of the dihedral angles a,a(X-C(1)-C(2)-X) from the idealized 180° are observed, accompanied by substantial flattening of the ring dihedral angles ρ(X-C(1)-C(2)-C(3)).
Ethyl 2-(4-meth-oxy-phen-yl)-6-oxa-3-aza-bicyclo[3.1.0]hexane-3-carboxyl-ate: crystal structure and Hirshfeld analysis.

PubMed

Zukerman-Schpector, Julio; Sugiyama, Fabricia H; Garcia, Ariel L L; Correia, Carlos Roque D; Jotani, Mukesh M; Tiekink, Edward R T

2017-07-01

The title compound, C 14 H 17 NO 4 , features an epoxide-O atom fused to a pyrrolidyl ring, the latter having an envelope conformation with the N atom being the flap. The 4-meth-oxy-phenyl group is orthogonal to [dihedral angle = 85.02 (6)°] and lies to the opposite side of the five-membered ring to the epoxide O atom, while the N-bound ethyl ester group (r.m.s. deviation of the five fitted atoms = 0.0187 Å) is twisted with respect to the ring [dihedral angle = 17.23 (9)°]. The most prominent inter-actions in the crystal are of the type methine-C-H⋯O(carbon-yl) and these lead to the formation of linear supra-molecular chains along the c axis; weak benzene-C-H⋯O(epoxide) and methine-C-H⋯O(meth-oxy) inter-actions connect these into a three-dimensional architecture. The analysis of the Hirshfeld surface confirms the presence of C-H⋯O inter-actions in the crystal, but also the dominance of H⋯H dispersion contacts.
(S)-2-(Iodo-meth-yl)-1-tosyl-pyrrolidine.

PubMed

Wang, Ya-Wen; Peng, Yu

2007-12-06

In the title mol-ecule, C(12)H(16)INO(2)S, the pyrrolidine ring is in an envelope conformation. The dihedral angle between the four essentially coplanar atoms of the pyrrolidine ring and the benzene ring is 75.5 (4)°.
High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.

PubMed

Haxton, Thomas K

2015-03-10

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme retains nearly atomistic resolution by mapping all experimental protein configurations in the Protein Data Bank onto coarse-grained configurations and then analytically backmapping those configurations back to all-atom configurations. This roundtrip mapping throws away all information associated with the eliminated (stiff) degrees of freedom except for their average values, which we use to construct optimal backmapping functions. Despite the 4:1 reduction in the number of degrees of freedom, we find that heavy atoms move only 0.051 Å on average during the roundtrip mapping, while hydrogens move 0.179 Å on average, an unprecedented combination of efficiency and accuracy among coarse-grained protein models. We discuss the advantages of such a high-resolution model for parametrizing effective interactions and accurately calculating observables through direct or multiscale simulations.
Tri-p-tolylphosphine

PubMed Central

Wang, Hao; Wang, Yi-Bin; Liu, Bo-Nian; Tang, Shi-Gui; Wei, Ping

2008-01-01

In the title compound C21H21P, the P atom is situated on a crystallographic threefold rotatory-inversion axis, resulting in threefold rotation symmetry of the title compound. The dihedral angles between the symmetry-related benzene rings are 87.40 (18)°. PMID:21201763
(Z)-3-Methyl-4-[1-(4-methylanilino)propylidene]-1-phenyl-1H-pyrazol-5(4H)-one

PubMed Central

Sharma, Naresh; Vyas, Komal M.; Jadeja, R. N.; Kant, Rajni; Gupta, Vivek K.

2013-01-01

In the title molecule, C20H21N3O, the central pyrazole ring forms dihedral angles of 4.75 (9) and 49.11 (9)°, respectively, with the phenyl and methyl-substituted benzene rings. The dihedral angle between the phenyl and benzene rings is 51.76 (8)°. The amino group and carbonyl O atom are involved in an intramolecular N—H⋯O hydrogen bond. In the crystal, π–π interactions are observed between benzene rings [centroid–centroid seperation = 3.892 (2) Å] and pyrazole rings [centroid–centroid seperation = 3.626 (2) Å], forming chains along [111]. The H atoms of the methyl group on the p-tolyl substituent were refined as disordered over two sets of sites in a 0.60 (4):0.40 (4) ratio. PMID:24109353
N-(1-Allyl-1H-indazol-5-yl)-4-meth-oxy-benzene-sulfonamide hemihydrate.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Geffken, Detlef; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

In the title compound, C17H17N3O3 (.)0.5H2O, the indazole system makes a dihedral angle of 46.19 (8)° with the plane through the benzene ring and is nearly perpendicular to the allyl group, as indicated by the dihedral angle of 81.2 (3)°. In the crystal, the water mol-ecule, disordered over two sites related by an inversion center, forms O-H⋯N bridges between indazole N atoms of two sulfonamide mol-ecules. It is also connected via N-H⋯O inter-action to the third sulfonamide mol-ecule; however, due to the water mol-ecule disorder, only every second mol-ecule of sulfonamide participates in this inter-action. This missing inter-action results in a slight disorder of the sulfonamide S,O and N atoms which are split over two sites with half occupancy. With the help of C-H⋯O hydrogen bonds, the mol-ecules are further connected into a three-dimensional network.

14 CFR 25.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2010 CFR

2010-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first... two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the... axis. (d) Dihedral angle A (aft) is formed by two intersecting vertical planes making angles of 70...
14 CFR 27.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2010 CFR

2010-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first... two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and... longitudinal axis. (d) Dihedral angle A (aft) is formed by two intersecting vertical planes making angles of 70...
Dependence of short and intermediate-range order on preparation in experimental and modeled pure a-Si

DOE PAGES

Holmstrom, Eero; Haberl, Bianca; Pakarinen, Olli H.; ...

2016-02-20

Variability in the short-to-intermediate range order of pure amorphous silicon prepared by different experimental and computational techniques is probed by measuring mass density, atomic coordination, bond-angle deviation, and dihedral angle deviation. It is found that there is significant variability in order parameters at these length scales in this archetypal covalently bonded, monoatomic system. This diversity strongly reflects preparation technique and thermal history in both experimental and simulated systems. Experiment and simulation do not fully quantitatively agree, partly due to differences in the way parameters are accessed. However, qualitative agreement in the trends is identified. Relaxed forms of amorphous silicon closelymore » resemble continuous random networks generated by a hybrid method of bond-switching Monte Carlo and molecular dynamics simulation. As-prepared ion implanted amorphous silicon can be adequately modeled using a structure generated from amorphization via ion bombardement using energetic recoils. Preparation methods which narrowly avoid crystallization such as experimental pressure-induced amorphization or simulated melt-quenching result in inhomogeneous structures that contain regions with significant variations in atomic ordering. Ad hoc simulated structures containing small (1 nm) diamond cubic crystal inclusions were found to possess relatively high bond-angle deviations and low dihedral angle deviations, a trend that could not be reconciled with any experimental material.« less
Normal Mode Analysis of Polytheonamide B

NASA Astrophysics Data System (ADS)

Mori, Takaharu; Kokubo, Hironori; Shimizu, Hirofumi; Iwamoto, Masayuki; Oiki, Shigetoshi; Okamoto, Yuko

2007-09-01

Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating d- and l-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ,\\psi), and correlation factors for the Cα atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.
14 CFR 29.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2010 CFR

2010-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the... formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft... longitudinal axis. (d) Dihedral angle A (aft) is formed by two intersecting vertical planes making angles of 70...
14 CFR 23.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2010 CFR

2010-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the... formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane... longitudinal axis. (d) Dihedral angle A (aft) is formed by two intersecting vertical planes making angles of 70...
Crystal structure of (pyridine-κN)bis(quinolin-2-olato-κ2 N,O)copper(II) monohydrate

PubMed Central

Hawks, Benjamin; Yan, Jingjing; Basa, Prem; Burdette, Shawn

2015-01-01

The title complex, [Cu(C9H6NO)2(C5H4N)]·H2O, adopts a slightly distorted square-pyramidal geometry in which the axial pyridine ligand exhibits a long Cu—N bond of 2.305 (3) Å. The pyridine ligand forms dihedral angles of 79.5 (5) and 88.0 (1)° with the planes of the two quinolin-2-olate ligands, while the dihedral angle between the quinoline groups of 9.0 (3)° indicates near planarity. The water molecule connects adjacent copper complexes through O—H⋯O hydrogen bonds to phenolate O atoms, forming a network interconnecting all the complexes in the crystal lattice. PMID:25878845
Formation of a 1,4-diamino-2,3-disila-1,3-butadiene derivative.

PubMed

Mondal, Kartik Chandra; Roesky, Herbert W; Dittrich, Birger; Holzmann, Nicole; Hermann, Markus; Frenking, Gernot; Meents, Alke

2013-10-30

A 1,4-diamino-2,3-disila-1,3-butadiene derivative of composition (Me2-cAAC)2(Si2Cl2) (Me2-cAAC = :C(CMe2)2(CH2)N-2,6-iPr2C6H3) was synthesized by reduction of the Me2-cAAC:SiCl4 adduct with KC8. This compound is stable at 0 °C for 3 months in an inert atmosphere. Theoretical studies reveal that the silicon atoms exhibit pyramidal coordination, where the Cl-Si-Si-Cl dihedral angle is twisted by 43.3° (calcd 45.9°). The two silicon-carbon bonds are intermediates between single and double Si-C bonds due to twisting of the C-Si-Si-C dihedral angle (163.6°).
1,1′-Bis[bis(4-methoxyphenyl)phosphanyl]ferrocene

PubMed Central

Ren, Xinfeng; Wang, Le; Li, Ya

2012-01-01

In the crystal structure of the title substituted ferrocene complex, [Fe(C19H18O2P)2], the FeII atom lies on a twofold rotation axis, giving an eclipsed cyclopentadienyl conformation with a ring centroid separation of 3.292 (7) Å and an Fe—C bond-length range of 2.0239 (15)–2.0521 (15) Å. In the ligand, the cyclopentadienyl ring forms dihedral angles of 60.36 (6) and 82.93 (6)° with the two benzene rings of the diphenylphosphine group, while the dihedral angle between the benzene rings is 67.4 (5)°. PMID:22807756
(S)-2-(Iodomethyl)-1-tosylpyrrolidine

PubMed Central

Wang, Ya-Wen; Peng, Yu

2008-01-01

In the title molecule, C12H16INO2S, the pyrrolidine ring is in an envelope conformation. The dihedral angle between the four essentially coplanar atoms of the pyrrolidine ring and the benzene ring is 75.5 (4)°. PMID:21200932
2-Methyl-2-phenyl-1-(pyrrolidin-1-yl)propan-1-one.

PubMed

Ren, Dong-Mei

2013-05-01

In the title compound, C14H19NO, the dihedral angle between the benzene ring and the plane of the amide group is 80.6 (1)°. In the crystal, mol-ecules are connected via weak C-H⋯O hydrogen bonds, forming chains along the c-axis direction. The conformation of the five-memebred ring is an envelope, with one of the ring C atoms adjacent to the ring N atom as the flap atom.
Molecular structures of carotenoids as predicted by MNDO-AM1 molecular orbital calculations

NASA Astrophysics Data System (ADS)

Hashimoto, Hideki; Yoda, Takeshi; Kobayashi, Takayoshi; Young, Andrew J.

2002-02-01

Semi-empirical molecular orbital calculations using AM1 Hamiltonian (MNDO-AM1 method) were performed for a number of biologically important carotenoid molecules, namely all- trans-β-carotene, all- trans-zeaxanthin, and all- trans-violaxanthin (found in higher plants and algae) together with all- trans-canthaxanthin, all- trans-astaxanthin, and all- trans-tunaxanthin in order to predict their stable structures. The molecular structures of all- trans-β-carotene, all- trans-canthaxanthin, and all- trans-astaxanthin predicted based on molecular orbital calculations were compared with those determined by X-ray crystallography. Predicted bond lengths, bond angles, and dihedral angles showed an excellent agreement with those determined experimentally, a fact that validated the present theoretical calculations. Comparison of the bond lengths, bond angles and dihedral angles of the most stable conformer among all the carotenoid molecules showed that the displacements are localized around the substituent groups and hence around the cyclohexene rings. The most stable conformers of all- trans-zeaxanthin and all- trans-violaxanthin gave rise to a torsion angle around the C6-C7 bond to be ±48.7 and -84.8°, respectively. This difference is a key factor in relation to the biological function of these two carotenoids in plants and algae (the xanthophyll cycle). Further analyses by calculating the atomic charges and using enpartment calculations (division of bond energies between component atoms) were performed to ascribe the cause of the different observed torsion angles.
Calculated Hydride Donor Abilities of Five-Coordinate Transition Metal Hydrides [HM(diphosphine)2] (+) (M = Ni, Pd, Pt) as a Function of the Bite Angle and Twist Angle of Diphosphine Ligands

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

Nimlos, Mark R.; Chang, Christopher H.; Curtis, Calvin J.

2008-07-07

Density functional theory (BLYP and B3LYP) and the polarized continuum model (PCM-UA0) for solvation have been used to investigate the effect of bite angle (P-M-P) of diphosphine ligands and the dihedral or twist angle between diphosphine ligands on the hydride donor abilities of Ni, Pd, and Pt [HM(diphosphine)2]+ complexes. It is found that an increased bite angle for a given transition metal atom results in poorer hydride donor abilities. However, hydride donor abilities for these complexes also decrease as the size of the alkyl side groups on the phosphorus atom increase (Et > Me > H) and with the lengthmore » of the metal phosphorus bond (Ni > Pd = Pt). These trends correlate with an increase in the twist angle between the two diphosphine ligands, which increases from 0° for a square-planar configuration to 90° for a tetrahedral geometry. Shorter M-P bonds, larger substituents on the diphosphine ligands, and larger bite angles all result in increased steric interactions between diphosphine ligands and larger dihedral or twist angles between the diphosphine ligands. The twist angle correlates much more strongly with hydride donor abilities than do bite angles alone. As the twist angle increases, the hydride donor ability decreases in a linear fashion. A frontier orbital analysis has been carried out, and it is shown that the hydride donor ability of [HM(diphosphine)2]+ complexes is largely determined by the energy of the lowest unoccupied molecular orbital of the corresponding [M(diphosphine)2]2+ complex. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less
Calculated Hydride Donor Abilities of Five-Coordinate Transition Metal Hydrides [HM(diphosphine)2]+ (M = Ni, Pd, Pt) as a Function of the Bite Angle and Twist Angle of Diphosphine Ligands

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

Nimlos, Mark; Chang, Christopher H.; Curtis, Calvin J.

2008-06-23

Density functional theory (BLYP and B3LYP) and the polarized continuum model (PCM-UA0) for solvation have been used to investigate the effect of bite angle (P-M-P) of diphosphine ligands and the dihedral or twist angle between diphosphine ligands on the hydride donor abilities of Ni, Pd, and Pt [HM(diphosphine)2]+ complexes. It is found that an increased bite angle for a given transition metal atom results in poorer hydride donor abilities. However, hydride donor abilities for these complexes also decrease as the size of the alkyl side groups on the phosphorus atom increase (Et > Me > H) and with the lengthmore » of the metal phosphorus bond (Ni > Pd = Pt). These trends correlate with an increase in the twist angle between the two diphosphine ligands, which increases from 0° for a square-planar configuration to 90° for a tetrahedral geometry. Shorter M-P bonds, larger substituents on the diphosphine ligands, and larger bite angles all result in increased steric interactions between diphosphine ligands and larger dihedral or twist angles between the diphosphine ligands. The twist angle correlates much more strongly with hydride donor abilities than do bite angles alone. As the twist angle increases, the hydride donor ability decreases in a linear fashion. A frontier orbital analysis has been carried out, and it is shown that the hydride donor ability of [HM(diphosphine)2]+ complexes is largely determined by the energy of the lowest unoccupied molecular orbital of the corresponding [M(diphosphine)2]2+ complex. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less
N-(1-Allyl-1H-indazol-5-yl)-4-methoxybenzenesulfonamide hemihydrate

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Geffken, Detlef; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

In the title compound, C17H17N3O3 .0.5H2O, the indazole system makes a dihedral angle of 46.19 (8)° with the plane through the benzene ring and is nearly perpendicular to the allyl group, as indicated by the dihedral angle of 81.2 (3)°. In the crystal, the water molecule, disordered over two sites related by an inversion center, forms O—H⋯N bridges between indazole N atoms of two sulfonamide molecules. It is also connected via N—H⋯O interaction to the third sulfonamide molecule; however, due to the water molecule disorder, only every second molecule of sulfonamide participates in this interaction. This missing interaction results in a slight disorder of the sulfonamide S,O and N atoms which are split over two sites with half occupancy. With the help of C–H⋯O hydrogen bonds, the molecules are further connected into a three-dimensional network. PMID:24098264
Dihedral Angles As A Diagnostic Tool For Interpreting The Cooling History Of Mafic Rocks

NASA Astrophysics Data System (ADS)

Holness, M. B.

2016-12-01

The geometry of three-grain junctions in mafic rocks, particularly those involving two grains of plagioclase, overwhelmingly results from processes occurring during solidification. Sub-solidus textural modification is only significant for fine-grained rocks that have remained hot for a considerable time (e.g. chill zones). The underlying control on the geometry of junctions involving plagioclase is the response of the different plagioclase growth faces to changes in cooling rate. This is demonstrated by the systematic co-variation of plagioclase grain shape and the median value of the pyroxene-plag-plag dihedral angle across (unfractionated) mafic sills. In mafic layered intrusions the median dihedral angle is constant across large stretches of stratigraphy, changing in a step-wise manner as the number of liquidus phases changes in the bulk magma. In the Skaergaard layered intrusion, the shape of cumulus plagioclase grains changes smoothly through the stratigraphy, consistent with continuously decreasing cooling rates in a well-mixed chamber: there is no correlation between overall plagioclase grain shape and dihedral angle. However, three-grain junctions are formed during the last stages of crystallization and therefore record events at the base of the crystal mushy layer. While the overall shape of plagioclase grains is dominated by growth at the magma-mush interface or in the bulk magma, it is the post-accumulation overgrowth that creates the dihedral angle: the shape of this overgrowth changes in a step-wise fashion, matching the step-wise variation in dihedral angle. Dihedral angles in layered intrusions can be used to place constraints on the thickness of the mushy layer, using the stratigraphic offset between the step-wise change in dihedral angle and the first appearance/disappearance of the associated liquidus phase. Dihedral angles also have the potential to constrain intrusion size for fragments of cumulate rocks entrained in volcanic ejecta.
Novel concept of enzyme selective nicotinamide adenine dinucleotide (NAD)-modified inhibitors based on enzyme taxonomy from the diphosphate conformation of NAD.

PubMed

Fujii, Mikio; Kitagawa, Yasuyuki; Iida, Shui; Kato, Keisuke; Ono, Machiko

2015-11-15

The dihedral angle θ of the diphosphate part of NAD(P) were investigated to distinguish the differences in the binding-conformation of NAD(P) to enzymes and to create an enzyme taxonomy. Furthermore, new inhibitors with fixed dihedral angles showed that enzymes could recognize the differences in the dihedral angle θ. We suggest the taxonomy and the dihedral angle θ are important values for chemists to consider when designing inhibitors and drugs that target enzymes. Copyright © 2015 Elsevier Ltd. All rights reserved.
2-(Naphthalen-1-yl)-4-(naphthalen-1-ylmethylidene)-1,3-oxazol-5(4H)-one

PubMed Central

Gündoğdu, Cevher; Alp, Serap; Ergün, Yavuz; Tercan, Barış; Hökelek, Tuncer

2011-01-01

In the title compound, C24H15NO2, the oxazole ring is oriented at dihedral angles of 10.09 (4) and 6.04 (4)° with respect to the mean planes of the naphthalene ring systems, while the two naphthalene ring systems make a dihedral angle of 4.32 (3)°. Intramolecular C—H⋯N hydrogen bonds link the oxazole N atom to the naphthalene ring systems. In the crystal, intermolecular weak C—H⋯O hydrogen bonds link the molecules into centrosymmetric dimers. π–π contacts between the oxazole and naphthalene rings and between the naphthalene ring systems [centroid–centroid distances = 3.5947 (9) and 3.7981 (9) Å] may further stabilize the crystal structure. Three weak C—H⋯π interactions also occur. PMID:21754548
Accurate Analysis of Target Characteristic in Bistatic SAR Images: A Dihedral Corner Reflectors Case.

PubMed

Ao, Dongyang; Li, Yuanhao; Hu, Cheng; Tian, Weiming

2017-12-22

The dihedral corner reflectors are the basic geometric structure of many targets and are the main contributions of radar cross section (RCS) in the synthetic aperture radar (SAR) images. In stealth technologies, the elaborate design of the dihedral corners with different opening angles is a useful approach to reduce the high RCS generated by multiple reflections. As bistatic synthetic aperture sensors have flexible geometric configurations and are sensitive to the dihedral corners with different opening angles, they specially fit for the stealth target detections. In this paper, the scattering characteristic of dihedral corner reflectors is accurately analyzed in bistatic synthetic aperture images. The variation of RCS with the changing opening angle is formulated and the method to design a proper bistatic radar for maximizing the detection capability is provided. Both the results of the theoretical analysis and the experiments show the bistatic SAR could detect the dihedral corners, under a certain bistatic angle which is related to the geometry of target structures.
Accurate Analysis of Target Characteristic in Bistatic SAR Images: A Dihedral Corner Reflectors Case

PubMed Central

Ao, Dongyang; Hu, Cheng; Tian, Weiming

2017-01-01

The dihedral corner reflectors are the basic geometric structure of many targets and are the main contributions of radar cross section (RCS) in the synthetic aperture radar (SAR) images. In stealth technologies, the elaborate design of the dihedral corners with different opening angles is a useful approach to reduce the high RCS generated by multiple reflections. As bistatic synthetic aperture sensors have flexible geometric configurations and are sensitive to the dihedral corners with different opening angles, they specially fit for the stealth target detections. In this paper, the scattering characteristic of dihedral corner reflectors is accurately analyzed in bistatic synthetic aperture images. The variation of RCS with the changing opening angle is formulated and the method to design a proper bistatic radar for maximizing the detection capability is provided. Both the results of the theoretical analysis and the experiments show the bistatic SAR could detect the dihedral corners, under a certain bistatic angle which is related to the geometry of target structures. PMID:29271917

7-Chloro-4-[(7-chloroquinolin-4-yl)sulfanyl]quinoline dihydrate

PubMed Central

Wardell, James L.; Tiekink, Edward R. T.

2012-01-01

In the title thioether dihydrate, C18H10Cl2N2S·2H2O, the S-bound quinolinyl residues are almost orthogonal, forming a dihedral angle of 72.36 (4)°. In the crystal, the four water molecules are connected via an eight-membered {⋯OH}4 synthon with each of the four pendent water H atoms hydrogen bonded to a pyridine N atom to stabilize a three-dimensional architecture. PMID:22589973
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.
RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning.

PubMed

Gao, Yujuan; Wang, Sheng; Deng, Minghua; Xu, Jinbo

2018-05-08

Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary structure prediction. However, direct angle prediction from sequence alone is challenging. In this article, we present a novel method (named RaptorX-Angle) to predict real-valued angles by combining clustering and deep learning. Tested on a subset of PDB25 and the targets in the latest two Critical Assessment of protein Structure Prediction (CASP), our method outperforms the existing state-of-art method SPIDER2 in terms of Pearson Correlation Coefficient (PCC) and Mean Absolute Error (MAE). Our result also shows approximately linear relationship between the real prediction errors and our estimated bounds. That is, the real prediction error can be well approximated by our estimated bounds. Our study provides an alternative and more accurate prediction of dihedral angles, which may facilitate protein structure prediction and functional study.
Crystal structure of (E)-N′-{[(1R,3R)-3-isopropyl-1-methyl-2-oxocyclopentyl]methylidene}-4-methylbenzenesulfonohydrazide

PubMed Central

Tymann, David; Dragon, Dina Christina; Golz, Christopher; Preut, Hans; Strohmann, Carsten; Hiersemann, Martin

2015-01-01

The title compound, C17H24N2O3S, was synthesized in order to determine the relative configuration of the corresponding β-keto aldehyde. In the U-shaped molecule, the five-membered ring approximates an envelope with the methylene atom adjacent to the quaternary C atom being the flap. The dihedral angles between the four nearly coplanar atoms of the five-membered ring and the flap and the aromatic ring are 38.8 (4) and 22.9 (2)°, respectively. The bond angles around the S atom are in the range 104.11 (16)–119.95 (16)°. In the crystal, molecules are linked via N—H⋯O by hydrogen bonds, forming a chain along the a-axis direction. PMID:25878892
N-[2-(5-Bromo-2-morpholin-4-ylpyrimidin-4-ylsulfanyl)-4-methoxyphenyl]-2,4,6-trimethylbenzenesulfonamide

PubMed Central

Kumar, Mohan; Mallesha, L.; Sridhar, M. A.; Kapoor, Kamini; Gupta, Vivek K.; Kant, Rajni

2012-01-01

In the title compound, C24H27BrN4O4S2, the molecule is twisted at the sulfonyl S atom with a C—S(O2)—N(H)—C torsion angle of 62.6 (3)°. The benzene rings bridged by the sulfonamide group are tilted to each other by a dihedral angle of 60.6 (1)°. The dihedral angle between the sulfur-bridged pyrimidine and benzene rings is 62.7 (1)°. The morpholine ring adopts a chair conformation. The molecular conformation is stabilized by a weak intramolecular π–π stacking interaction between the pyrimidine and the 2,4,6-trimethylbenzene rings [centroid–centroid distance = 3.793 (2) Å]. In the crystal, molecules are linked by N—H⋯O hydrogen bonds into a chain along the b axis. PMID:23284396
Bis[2-(hy-droxy-imino-meth-yl)phenolato]nickel(II): a second monoclinic polymorph.

PubMed

Rusanova, Julia A; Buvaylo, Elena A; Rusanov, Eduard B

2011-01-15

The title compound, [Ni(C(7)H(6)NO(2))(2)], (I), is a second monoclinic polymorph of the compound, (II), reported by Srivastava et al. [Acta Cryst. (1967), 22, 922] and Mereiter [Private communication (2002) CCDC refcode NISALO01]. The bond lengths and angles are similar in both structures. The mol-ecule in both structures lies on a crystallographic inversion center and both have an inter-nal hydrogen bond. The title compound crystallizes in the space group P2(1)/c (Z = 2), whereas compound (II) is in the space group P2(1)/n (Z = 2) with a similar cell volume but different cell parameters. In both polymorphs, mol-ecules are arranged in the layers but in contrast to the previously published compound (II) where the dihedral angle between the layers is 86.3°, in the title polymorph the same dihedral angle is 29.4°. The structure of (I) is stabilized by strong intra-molecular O-H⋯O hydrogen bonding between the O-H group and the phenolate O atom.
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.

PubMed

Lyons, James; Dehzangi, Abdollah; Heffernan, Rhys; Sharma, Alok; Paliwal, Kuldip; Sattar, Abdul; Zhou, Yaoqi; Yang, Yuedong

2014-10-30

Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between C(αi-1)-C(αi)-C(αi+1) (θ) and a dihedral angle rotated about the C(αi)-C(αi+1) bond (τ). θ and τ angles, as the representative of structural properties of three to four amino-acid residues, offer a description of backbone conformations that is complementary to φ and ψ angles (single residue) and secondary structures (>3 residues). Here, we report the first machine-learning technique for sequence-based prediction of θ and τ angles. Predicted angles based on an independent test have a mean absolute error of 9° for θ and 34° for τ with a distribution on the θ-τ plane close to that of native values. The average root-mean-square distance of 10-residue fragment structures constructed from predicted θ and τ angles is only 1.9Å from their corresponding native structures. Predicted θ and τ angles are expected to be complementary to predicted ϕ and ψ angles and secondary structures for using in model validation and template-based as well as template-free structure prediction. The deep neural network learning technique is available as an on-line server called Structural Property prediction with Integrated DEep neuRal network (SPIDER) at http://sparks-lab.org. Copyright © 2014 Wiley Periodicals, Inc.
Using Molecular Models To Show Steric Clash in Peptides: An Illustration of Two Disallowed Regions in the Ramachandran Diagram

ERIC Educational Resources Information Center

Halkides, Christopher J.

2013-01-01

In this activity, students manipulate three-dimensional molecular models of the Ala-Ala-Ala tripeptide, where Ala is alanine. They rotate bonds to show that the pairs of dihedral angles phi = 0 degrees, psi = 180 degrees, and phi = 0 degrees, psi = 0 degrees lead to unfavorable interactions among the main chain atoms of the tripeptide. This…
Measurement of local structural configurations associated with reversible photostructural changes in arsenic trisulfide films

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

Yang, C.Y.; Paesler, M.A.; Sayers, D.E.

1987-12-15

Extended x-ray-absorption fine-structure measurements have been made on three reversible and reproducible cycles of thermally annealed and light-soaked amorphous As/sub 2/S/sub 3/ films. Associated with the light-soaked material are (1) a very small increase in the population of wrong bonds in the first shell, (2) an enlarged As: S: As bond angle with an expansion of As: As distance in the second shell, (3) a larger spread in the distribution of As: S: As bond angles, and (4) an absence of any change in the third As: S shell. From these data, we present the first quantitative correlation between observedmore » local atomic structural changes and measured macroscopic properties that are associated with photodarkening. Our data demonstrate that the photoinduced structural changes mainly involve bonding alterations at S atoms as well as a change in the dihedral angle relationship between adjacent AsS/sub 3/ pyramids joined at S atoms.« less
N′-[(E)-3-Chloro-2-fluorobenzylidene]-6-methylnicotinohydrazide monohydrate

PubMed Central

Fun, Hoong-Kun; Quah, Ching Kheng; Shyma, P. C.; Kalluraya, Balakrishna; Vidyashree, J. H. S.

2012-01-01

The title compound, C14H11ClFN3O·H2O, exists in an E conformation with respect to the N=C bond. The pyridine ring forms a dihedral angle of 5.00 (9)° with the benzene ring. In the crystal, the ketone O atom accepts one O—H⋯O and one C—H⋯O hydrogen bond, the water O atom accepts one N—H⋯O and two C—H⋯O hydrogen bonds and the pyridine N atom accepts one O—H⋯N hydrogen bond, forming layers parallel to the ab plane. PMID:22798798
The mechanism of the emergence of distinct overstretched DNA states

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

Zhu, You-Liang; Sun, Zhao-Yan, E-mail: zysun@ciac.ac.cn; Lu, Zhong-Yuan

Although multiple overstretched DNA states were identified in experiments, the mechanism of the emergence of distinct states is still unclear. Molecular dynamics simulation is an ideal tool to clarify the mechanism, but the force loading rates in stretching achieved by conventional all-atom DNA models are much faster, which essentially affect overstretching states. We employed a modified coarse-grained DNA model with an unprecedented low loading rate in simulations to study the overstretching transitions of end-opened double-stranded DNA. We observed two-strand peeling off for DNA with low stability and the S-DNA with high stability under tension. By introducing a melting-forbidden model whichmore » prevents base-pair breaking, we still observed the overstretching transition induced by the formation of S-DNA due to the change of dihedral angle. Hence, we confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states.« less
Ensemble of Transition State Structures for the Cis-Trans Isomerization of N-Methylacetamide

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

Mantz, Yves A.; Branduardi, Davide; Bussi, Giovanni

2009-09-17

The cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verifiedmore » by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms.« less
Biomolecular Chemistry of Isopropyl Fibrates

PubMed Central

Rath, Niharika; Kotheimer, Amenda; Miller, Chad; Zeller, Matthias; Rath, Nigam P.

2012-01-01

Isopropyl 2-[4-(4-chlorobenzoyl)-phenoxy]-2-methylpropanoic acid and isopropyl 2-(4-chlorophenoxy)-2-methylpropanoate, also known as fenofibrate and isopropyl clofibrate, are hypolipidemic agents of the fibrate family. In a previously reported triclinic structure of fenofibrate (polymorph I) the methyl groups of the isopropyl moiety (iPr) are located symmetrically about the carboxylate group. We report a new monoclinic form (polymorph II) of fenofibrate and a first structural description of isopropyl clofibrate, and in these the methyl groups are placed asymmetrically about the carboxylate group. In particular the dihedral (torsion) angle between the hydrogen atom on the secondary C and the C atom of the carboxyl group makes a 2.74° angle about the ester O-C bond in the symmetric fenofibrate structure of polymorph I, whereas the same dihedral angle is 45.94° in polymorph II and -30.9° in the crystal structure of isopropyl clofibrate. Gas phase DFT geometry minimizations of fenofibrate and isopropyl clofibrate result in lowest energy conformations for both molecules with a value of about ± 30° for this same angle between the O=C-O-C plane and the C-H bond of the iPr group. A survey of crystal structures containing an iPr ester group reveals that the asymmetric conformation is predominant. Although the hydrogen atom on the secondary C atom of the isopropyl group is located at a comparable distance from the carbonyl oxygen in the symmetric and asymmetric fenofibrate (2.52 and 2.28 Å) and the isopropyl clofibrate (2.36 Å) structures, this hydrogen atom participates in a puckered five membered ring arrangement in the latter two that is unlike the planar arrangement found in symmetric fenofibrate (polymorph I). Polar molecular surface area (PSA) values indicate fenofibrate and isopropyl clofibrate are less able to act as acceptors of hydrogen bonds than their corresponding acid derivatives. Surface area calculations show dynamic polar molecular surface area (PSAd) values of the iPr esters of the fibrates are lower than those of their acids, implying that the fibrates have better membrane permeability and a higher absorbability and hence are better prodrugs when these agents need to be orally administered. PMID:22246648
Dihedral angle principal component analysis of molecular dynamics simulations.

PubMed

Altis, Alexandros; Nguyen, Phuong H; Hegger, Rainer; Stock, Gerhard

2007-06-28

It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {phi(n)} to the metric coordinate space {x(n)=cos phi(n),y(n)=sin phi(n)} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300 ns molecular dynamics simulation, a critical comparison of the various methods is given.
Dihedral angle principal component analysis of molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Altis, Alexandros; Nguyen, Phuong H.; Hegger, Rainer; Stock, Gerhard

2007-06-01

It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {φn} to the metric coordinate space {xn=cosφn,yn=sinφn} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300ns molecular dynamics simulation, a critical comparison of the various methods is given.
Electric Dipole-Magnetic Dipole Polarizability and Anapole Magnetizability of Hydrogen Peroxide as Functions of the HOOH Dihedral Angle.

PubMed

Pelloni, S; Provasi, P F; Pagola, G I; Ferraro, M B; Lazzeretti, P

2017-12-07

The trace of tensors that account for chiroptical response of the H 2 O 2 molecule is a function of the HO-OH dihedral angle. It vanishes at 0° and 180°, due to the presence of molecular symmetry planes, but also for values in the range 90-100° of this angle, in which the molecule is unquestionably chiral. Such an atypical effect is caused by counterbalancing contributions of diagonal tensor components with nearly maximal magnitude but opposite sign, determined by electron flow in open or closed helical paths, and associated with induced electric and magnetic dipole moments and anapole moments. For values of dihedral angle external to the 90-100° interval, the helical paths become smaller in size, thus reducing the amount of cancellation among diagonal components. Shrinking of helical paths determines the appearance of extremum values of tensor traces approximately at 50° and 140° dihedral angles.
Sterically allowed configuration space for amino acid dipeptides

NASA Astrophysics Data System (ADS)

Caballero, Diego; Maatta, Jukka; Sammalkorpi, Maria; O'Hern, Corey; Regan, Lynne

2014-03-01

Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic propensities for amino acids to be in particular backbone or side-chain conformations. This question has remained unsettled for years because of the discrepancies between different experimental approaches. To address it, I performed all-atom hard-sphere simulations of hydrophobic residues with stereo-chemical constraints and non-attractive steric interactions between non-bonded atoms for ALA, ILE, LEU and VAL dipeptide mimetics. For these hard-sphere MD simulations, I show that transitions between α-helix and β-sheet structures only occur when the bond angle τ(N -Cα - C) >110° , and the probability distribution of bond angles for structures in the `bridge' region of ϕ- ψ space is shifted to larger angles compared to that in other regions. In contrast, the relevant bond-angle distributions obtained from most molecular dynamics packages are broader and shifter to larger values. I encounter similar correlations between bond angles and side-chain dihedral angles. The success of these studies is an argument for re-incorporating local stereochemical constraints into computational protein design methodology.
Crystal structure of allylammonium hydrogen succinate at 100 K

PubMed Central

Dziuk, Błażej; Zarychta, Bartosz; Ejsmont, Krzysztof

2014-01-01

The asymmetric unit of the title compound, C2H8N+·C4H5O4 −, consists of two allylammonium cations and two hydrogen succinate anions (Z′ = 2). One of the cations has a near-perfect syn-periplanar (cis) conformation with an N—C—C—C torsion angle of 0.4 (3)°, while the other is characterized by a gauche conformation and a torsion angle of 102.5 (3)°. Regarding the anions, three out of four carboxilic groups are twisted with respect to the central C–CH2–CH2–C group [dihedral angles = 24.4 (2), 31.2 (2) and 40.4 (2)°], the remaining one being instead almost coplanar, with a dihedral angle of 4.0 (2)°. In the crystal, there are two very short, near linear O—H⋯O hydrogen bonds between anions, with the H atoms shifted notably from the donor O towards the O⋯O midpoint. These O—H⋯O hydrogen bonds form helical chains along the [011] which are further linked to each other through N—H⋯O hydrogen bonds (involving all the available NH groups), forming layers lying parallel to (100). PMID:25309251
Crystal structure of N′-[(E)-(1S,3R)-(3-isopropyl-1-methyl-2-oxocyclopentyl)methylidene]-4-methylbenzenesulfonohydrazide

PubMed Central

Tymann, David; Dragon, Dina Christina; Golz, Christopher; Preut, Hans; Strohmann, Carsten; Hiersemann, Martin

2015-01-01

The title compound, C17H24N2O3S, was synthesized in order to determine the relative configuration of the corresponding β-keto aldehyde. In the U-shaped molecule, the five-membered ring approximates an envelope, with the methylene C atom adjacent to the quaternary C atom being the flap, and the methyl and isopropyl substituents lying to the same side of the ring. The dihedral angles between the four nearly coplanar atoms of the five-membered ring and the flap and the aromatic ring are 35.74 (15) and 55.72 (9)°, respectively. The bond angles around the S atom are in the range from 103.26 (12) to 120.65 (14)°. In the crystal, molecules are linked via N—H⋯O hydrogen bonds, forming a chain along the a axis. PMID:26870519
Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

PubMed

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

2016-01-01

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.
3-Phenylpyridinium tetrachloridoaurate(III)

PubMed Central

Amani, Vahid; Safari, Nasser; Khavasi, Hamid Reza

2010-01-01

In the title molecular salt, (C11H10N)[AuCl4], the AuIII atom adopts an almost regular square-planar coordination geometry and the dihedral angle between the aromatic rings of the 3-phenylpyridinium cation is 23.1 (3)°. In the crystal, the ions interact by way of N—H⋯Cl and C—H⋯Cl hydrogen bonds. PMID:21580276
Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

NASA Astrophysics Data System (ADS)

Shew, Christopher; Evans, Samari; Tao, Xiuping

How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.
What can the dihedral angle of conjugate-faults tell us?

NASA Astrophysics Data System (ADS)

Ismat, Zeshan

2015-04-01

Deformation within the upper crust (elastico-frictional regime) is largely accommodated by fractures and conjugate faults. The Coulomb fracture criterion leads us to expect that the average dihedral angle of conjugate-fault sets is expected to be ∼60°. Experiments, however, reveal a significant amount of scatter from this 60° average. The confining pressure under which these rocks are deformed is a contributing factor to this scatter. The Canyon Range syncline, Sevier fold-thrust belt (USA) and the Jebel Bani, Anti-Atlas fold-belt (Morocco) both folded under different depths, within the elastico-frictional regime, by cataclastic flow. Conjugate-fault sets assisted deformation by cataclastic flow. The Canyon Range syncline and the Jebel Bani are used here as natural examples to test the relationship between the dihedral angle of conjugate-faults and confining pressure. Variations is confining pressure are modeled by the difference in depth of deformation and position within the folds. Results from this study show that the dihedral angle increases with an increase in depth and within the hinge regions of folds, where space problems commonly occur. Moreover, the shortening directions based on the acute bisectors of conjugate-faults may not be accurately determined if the dihedral angles are unusually large or small, leading to incorrect kinematic analyses.
Dihedral angle control to improve the charge transport properties of conjugated polymers in organic field effect transistors

NASA Astrophysics Data System (ADS)

Dharmapurikar, Satej S.; Chithiravel, Sundaresan; Mane, Manoj V.; Deshmukh, Gunvant; Krishnamoorthy, Kothandam

2018-03-01

Diketopyrrolopyrrole (DPP) and i-Indigo (i-Ind) are two monomers that are widely explored as active materials in organic field effect transistor and solar cells. These two molecules showed impressive charge carrier mobility due to better packing that are facilitated by quadrupoles. We hypothesized that the copolymers of these monomers would also exhibit high charge carrier mobility. However, we envisioned that the dihedral angle at the connecting point between the monomers will play a crucial role in packing as well as charge transport. To understand the impact of dihedral angle on charge transport, we synthesized three copolymers, wherein the DPP was sandwiched between benzenes, thiophenes and furans. The copolymer of i-Indigo and furan comprising DPP showed a band gap of 1.4 eV with a very high dihedral angle of 179°. The polymer was found to pack better and the coherence length was found to be 112 Å. The hole carrier mobility of these polymer was found to be highest among the synthesized polymer i.e. 0.01 cm2/vs. The copolymer comprising benzene did not transport hole and electrons. The dihedral angle at the connecting point between i and Indigo and benzene DPP was 143 Å, which the packing and consequently charge transport properties.
A Uranyl Peroxide Dimer in the Gas Phase

DOE PAGES

Dau, Phuong D.; Dau, Phuong V.; Rao, Linfeng; ...

2017-03-14

For this study, the gas-phase uranyl peroxide dimer, [(UO 2) 2(O2)(L) 2] 2+ where L = 2,2'-trifluoroethylazanediyl)bis(N,N'-dimethylacetamide), was synthesized by electrospray ionization of a solution of UO 2 2+ and L. Collision-induced dissociation of this dimer resulted in endothermic O atom elimination to give [(UO 2) 2(O)(L) 2] 2+, which was found to spontaneously react with water via exothermic hydrolytic chemisorption to yield [(UO 2) 2(OH) 2(L) 2] 2+. Density functional theory computations of the energies for the gas-phase reactions are in accord with observations. The structures of the observed uranyl dimer were computed, with that of the peroxide ofmore » particular interest, as a basis to evaluate the formation of condensed phase uranyl peroxides with bent structures. The computed dihedral angle in [(UO 2) 2(O 2)(L) 2] 2+ is 145°, indicating a substantial deviation from the planar structure with a dihedral angle of 180°. Energies needed to induce bending in the most elementary gas-phase uranyl peroxide complex, [(UO 2) 2(O 2)] 2+, were computed. It was found that bending from the lowest-energy planar structure to dihedral angles up to 140° required energies of <10 kJ/mol. The gas-phase results demonstrate the inherent stability of the uranyl peroxide moiety and support the notion that the uranyl-peroxide-uranyl structural unit is intrinsically planar, with only minor energy perturbations needed to form the bent structures found in studtite and uranyl peroxide nanostructures.« less
Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.

PubMed

Banerjee, Rahul; Cukier, Robert I

2014-03-20

Conformational states and their interconversion pathways of the zwitterionic form of the pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular dynamics (MD) trajectory is used to construct a Markov state model (MSM) based on dihedral space clustering of the trajectory, and transition path theory (TPT) is applied to identify pathways between open and closed conformers. In the MD trajectory, only four of the eight backbone dihedrals exhibit bistable behavior. Defining a conformer as the string XXXX with X = "+" or "-" denoting, respectively, positive or negative values of a given dihedral angle and obtaining the populations of these conformers shows that only four conformers are highly populated, implying a strong correlation among these dihedrals. Clustering in dihedral space to construct the MSM finds the same four bistable dihedral angles. These state populations are very similar to those found directly from the MD trajectory. TPT is used to obtain pathways, parametrized by committor values, in dihedral state space that are followed in transitioning from closed to open states. Pathway costs are estimated by introducing a kinetics-based procedure that orders pathways from least (shortest) to greater cost paths. The least costly pathways in dihedral space are found to only involve the same XXXX set of dihedral angles, and the conformers accessed in the closed to open transition pathways are identified. For these major pathways, a correlation between reaction path progress (committors) and the end-to-end distance is identified. A dihedral space principal component analysis of the MD trajectory shows that the first three modes capture most of the overall fluctuation, and pick out the same four dihedrals having essentially all the weight in those modes. A MSM based on root-mean-square backbone clustering was also carried out, with good agreement found with dihedral clustering for the static information, but with results that differ significantly for the pathway analysis.
Bistatic 3D Electromagnetic Scattering From a Right-Angle Dihedral at Arbitrary Orientation and Position

DTIC Science & Technology

2011-03-24

compared to shooting and bouncing rays (SBR) and method of moments (MoM) predictions, as well as measured data for applicable cases. The model in this...prediction codes based on Shooting and Bouncing Rays (SBR) or Method of Moments (MoM) can be used to obtain accurate bistatic scatter- ing solutions for a...in-plane RCS pattern for dihedral. (a) For monostatic in-plane scattering, rays entering a right-angle dihedral are reflected back in the direction
A generalized technique for using cones and dihedral angles in attitude determination, revision 1

NASA Technical Reports Server (NTRS)

Werking, R. D.

1973-01-01

Analytic development is presented for a general least squares attitude determination subroutine applicable to spinning satellites. The method is founded on a geometric approach which is completely divorced from considerations relating to particular types and configurations of onboard attitude sensors. Any mix of sensor measurements which can be first transformed (outside the program) to cone or dihedral angle data can be processed. A cone angle is an angle between the spin axis and a known direction line in space; a dihedral angle is an angle between two planes formed by the spin axis and each of two known direction lines. Many different kinds of sensor data can be transformed to these angles, which in turn constitute the actual program inputs, so that the subroutine can be applied without change to a variety of satellite missions. Either a constant or dynamic spin axis model can be handled. The program is also capable of solving for fixed biases in the input angles, in addition to the spin axis attitude solution.
Control Mechanisms of Photoisomerization in Protonated Schiff Bases.

PubMed

Vuković, Lela; Burmeister, Carl F; Král, Petr; Groenhof, Gerrit

2013-03-21

We performed ab initio excited-state molecular dynamics simulations of a gas-phase photoexcited protonated Schiff base (C1-N2═C3-C4═C5-C6) to search for control mechanisms of its photoisomerization. The excited molecule twists by ∼90° around either the N2C3 bond or the C4C5 bond and relaxes to the ground electronic state through a conical intersection with either a trans or cis outcome. We show that a large initial distortion of several dihedral angles and a specific normal vibrational mode combining pyramidalization and double-bond twisting can lead to a preferential rotation of atoms around the C4C5 bond. We also show that selective pretwisting of several dihedral angles in the initial ground state thermal ensemble (by analogy to a protein pocket) can significantly increase the fraction of photoreactive (cis → trans) trajectories. We demonstrate that new ensembles with higher degrees of control over the photoisomerization reaction can be obtained by a computational directed evolution approach on the ensembles of molecules with the pretwisted geometries.
Crystal structure of benzyl 3-(3-methyl-phen-yl)di-thio-carbazate.

PubMed

Aziz, NurFadhilah Abdul; Yusof, Enis Nadia Md; Ravoof, Thahira Begum S A; Tiekink, Edward R T

2015-04-01

In the title compound, C15H16N2S2, the central CN2S2 residue is almost planar (r.m.s. deviation = 0.0354 Å) and forms dihedral angles of 56.02 (4) and 75.52 (4)° with the phenyl and tolyl rings, respectively; the dihedral angle between the aromatic rings is 81.72 (5)°. The conformation about the N-N bond is gauche [C-N-N-C = -117.48 (15)°]. Overall, the mol-ecule has the shape of the letter L. In the crystal packing, supra-molecular chains along the a axis are formed by N-H⋯S(thione) hydrogen bonds whereby the thione S atom accepts two such bonds. The hydrogen bonding leads to alternating edge-shared eight-membered {⋯HNCS}2 and 10-membered {⋯HNNH⋯S}2 synthons. The chains are connected into layers by phen-yl-tolyl C-H⋯π inter-actions; the layers stack along the c axis with no specific inter-actions between them.
Diaquabis(4-methoxybenzoato-κO 1)bis(nicotinamide-κN 1)cobalt(II) dihydrate

PubMed Central

Hökelek, Tuncer; Dal, Hakan; Tercan, Barış; Tenlik, Erdinç; Necefoğlu, Hacali

2010-01-01

In the mononuclear title compound, [Co(C8H7O3)2(C6H6N2O)2(H2O)2]·2H2O, the CoII ion is located on a crystallographic inversion center. The asymmetric unit is completed by one 4-methoxybenzoate anion, one nicotinamide (NA) ligand and one coordinated and one uncoordinated water molecule. All ligands act in a monodentate mode. The four O atoms in the equatorial plane around the CoII ion form a slightly distorted square-planar arrangement, while the slightly distorted octahedral coordination is completed by the two pyridine N atoms of the NA ligands in the axial positions. The dihedral angle between the carboxylate group and the attached benzene ring is 6.47 (7)°, while the pyridine and benzene rings are oriented at a dihedral angle of 72.80 (4)°. An O—H⋯O hydrogen bond links the uncoordinated water molecule to one of the carboxylate groups. In the crystal structure, intermolecular O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds link the molecules into a three-dimensional network. PMID:21588149
3-(6-Methyl-2-pyridyl)-2-phenyl-3,4-dihydro-1,3,2-benzoxazaphosphinine 2-oxide

PubMed Central

Surendra Babu, V. H. H.; Krishnaiah, M.; Anil Kumar, M.; Suresh Reddy, C.; Kant, Rajni

2009-01-01

In the title compound, C19H17N2O2P, the six-membered 1,3,2-oxazaphosphinine ring adopts a boat conformation with the phosphoryl O atom in an equatorial position. The dihedral angle between the 6-methyl-2-pyridyl and phenyl groups is 75.5 (1)°. These substituents are trans to each other, and are oriented at angles of 57.2 (1) and 74.8 (1)°, respectively, to the benzene ring. The crystal structure is stabilized by intra- and intermolecular hydrogen bonds. The phosphoryl O atom participates in intermolecular C—H⋯O interactions with the neighbouring molecules, forming centrosymmetric R 2 2(14) dimers. PMID:21578300
Quantitative evaluation of orbital hybridization in carbon nanotubes under radial deformation using π-orbital axis vector

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

Ohnishi, Masato, E-mail: masato.ohnishi@rift.mech.tohoku.ac.jp; Suzuki, Ken; Miura, Hideo, E-mail: hmiura@rift.mech.tohoku.ac.jp

2015-04-15

When a radial strain is applied to a carbon nanotube (CNT), the increase in local curvature induces orbital hybridization. The effect of the curvature-induced orbital hybridization on the electronic properties of CNTs, however, has not been evaluated quantitatively. In this study, the strength of orbital hybridization in CNTs under homogeneous radial strain was evaluated quantitatively. Our analyses revealed the detailed procedure of the change in electronic structure of CNTs. In addition, the dihedral angle, the angle between π-orbital axis vectors of adjacent atoms, was found to effectively predict the strength of local orbital hybridization in deformed CNTs.
Quantum chemical calculations of Cr2O3/SnO2 using density functional theory method

NASA Astrophysics Data System (ADS)

Jawaher, K. Rackesh; Indirajith, R.; Krishnan, S.; Robert, R.; Das, S. Jerome

2018-03-01

Quantum chemical calculations have been employed to study the molecular effects produced by Cr2O3/SnO2 optimised structure. The theoretical parameters of the transparent conducting metal oxides were calculated using DFT / B3LYP / LANL2DZ method. The optimised bond parameters such as bond lengths, bond angles and dihedral angles were calculated using the same theory. The non-linear optical property of the title compound was calculated using first-order hyperpolarisability calculation. The calculated HOMO-LUMO analysis explains the charge transfer interaction between the molecule. In addition, MEP and Mulliken atomic charges were also calculated and analysed.
Tri-μ-oxido-bis[(5,10,15,20-tetraphenylporphyrinato-κ4 N)niobium(V)

PubMed Central

Soury, Raoudha; Belkhiria, Mohamed Salah; Daran, Jean-Claude; Nasri, Habib

2011-01-01

In the title dinuclear NbV compound, [Nb2(C44H28N4)2O3], each Nb atom is seven-coordinated with three bridging O atoms and four N atoms from a chelating tetraphenylporphyrinate anion. The Nb—O bond lengths range from 1.757 (6) to 2.331 (6) Å, and the average (niobium–pyrrole N atom) distance is 2.239 Å. In the dinuclear molecule, the Nb⋯Nb separation is 2.8200 (8) Å, and the dihedral angle between the two porphyrinate mean planes is 5.4 (1)°. Weak intermolecular C—H⋯π interactions are present in the crystal structure. PMID:21836860
[1,1′-Diphenyl-3,3′-(propane-1,3-diyldinitrilo)dibut-1-enolato]copper(II)

PubMed Central

Salehi, Mehdi; Meghdadi, Soraia; Amirnasr, Mehdi; Mereiter, Kurt

2009-01-01

The title compound, [Cu(C23H24N2O2)] or [Cu{(BA)2pn}], where (BA)2pn is 1,1′-diphenyl-3,3′-(propane-1,3-diyldinitrilo)dibut-1-enolate, is a mononuclear copper(II) complex, located on a twofold axis. The four-coordinate CuII atom is in a tetrahedrally distorted square plane defined by the N and O atoms of the Schiff base ligand. In the tetradentate ligand, the two chelate rings are twisted relative to each other, making a dihedral angle of 36.57 (3)°. PMID:21581795
1-Do-decyl-indoline-2,3-dione.

PubMed

Qachchachi, Fatima-Zahrae; Ouazzani Chahdi, Fouad; Misbahi, Houria; Bodensteiner, Michael; El Ammari, Lahcen

2014-02-01

The structure of the title compound, C20H29NO2, is isotypic to that of its homologue 1-octylindoline-2,3-dione. The indoline ring and the two carbonyl-group O atoms are approximately coplanar, the largest deviation from the mean plane being 0.0760 (10) Å. The mean plane through the fused-ring system is nearly perpendicular to the mean plane passing through the 1-dodecyl chain [dihedral angle = 77.69 (5)°]. All C atoms of the dodecyl group are in an anti-periplanar arrangement. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming a three-dimensional network.
Proline-induced kink in a helix arises primarily from dihedral angle energy: a molecular dynamics simulation on alamethicin

NASA Astrophysics Data System (ADS)

Cheng, Shu-Fang; Chang, Ding-Kwo

1999-03-01

To investigate the cause of the kink in a helix induced by proline, a restrained molecular dynamics simulation was performed on alamethicin (Alm), a channel-forming peptide. Results on the linear and kinked helices indicated that the kinked form has lower energy than the linear one and the difference can be attributed largely to the dihedral angle term. The argument is strengthened by calculated results on the peptide in which proline 14 was substituted by alanine. The kinked and linear forms had virtually the same total and dihedral angle energies for the alanine analog. Possible implications for Alm voltage-gating are discussed.
Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation

PubMed Central

Das, Amit; Chakrabarti, J.; Ghosh, Mahua

2013-01-01

We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically. PMID:23528087

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.
14 CFR 25.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2012 CFR

2012-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the other at 110 degrees to the left of the first... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 27.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2014 CFR

2014-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and the other at 110 degrees to the left of the first... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 27.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2013 CFR

2013-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and the other at 110 degrees to the left of the first... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 27.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2012 CFR

2012-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and the other at 110 degrees to the left of the first... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 29.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2012 CFR

2012-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and the other at 110 degrees to the left of... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 23.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2013 CFR

2013-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the other at 110 degrees to the left of the... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 25.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2011 CFR

2011-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the other at 110 degrees to the left of the first... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 23.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2014 CFR

2014-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the other at 110 degrees to the left of the... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 25.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2013 CFR

2013-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the other at 110 degrees to the left of the first... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 27.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2011 CFR

2011-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and the other at 110 degrees to the left of the first... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 29.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2011 CFR

2011-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and the other at 110 degrees to the left of... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 25.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2014 CFR

2014-01-01

... this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the other at 110 degrees to the left of the first... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 29.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2013 CFR

2013-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and the other at 110 degrees to the left of... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 23.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2012 CFR

2012-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the other at 110 degrees to the left of the... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 23.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2011 CFR

2011-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the airplane, and the other at 110 degrees to the left of the... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
14 CFR 29.1387 - Position light system dihedral angles.

Code of Federal Regulations, 2014 CFR

2014-01-01

... described in this section. (b) Dihedral angle L (left) is formed by two intersecting vertical planes, the first parallel to the longitudinal axis of the rotorcraft, and the other at 110 degrees to the left of... degrees to the right and to the left, respectively, to a vertical plane passing through the longitudinal...
Investigation of a van der Waals complex with C 1 symmetry: the free-jet rotational spectrum of 1,2-difluoroethane-Ar

NASA Astrophysics Data System (ADS)

Melandri, Sonia; Velino, Biagio; Favero, Paolo G.; Dell'Erba, Adele; Caminati, Walther

2000-04-01

The van der Waals complex between Ar and 1,2-difluoroethane has been investigated by free-jet absorption millimeter-wave spectroscopy in the frequency range 60-78 GHz. The analysis of the spectroscopic constants derived from the rotational spectrum allowed the determination of the dimer's structure. 1,2-Difluoroethane is in the gauche conformation and the Ar atom is in a position stabilized by the interaction with one fluorine and the two carbon atoms. The distance between Ar and the center of mass (CM) of the monomer is 3.968 Å, the angle between the Ar-CM line and the C-C bond is 65° and the dihedral angle Ar-CM-C-C is 99°. From centrifugal distortion effects the dissociation energy of the complex has been estimated to be 2.1 kJ/mol.
N-(2-Allyl-4-chloro-2H-indazol-5-yl)-4-methoxybenzenesulfonamide hemihydrate

PubMed Central

Chicha, Hakima; Kouakou, Assoman; Rakib, El Mostapha; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

The fused five- and six-membered rings in the title compound, C17H16ClN3O3S·0.5H2O, are practically coplanar, with the maximum deviation from the mean plane being 0.057 (3) Å for the C atom bound to the exocyclic N atom. The indazole system makes a dihedral angle of 66.18 (12)° with the plane through the benzene ring, and it is nearly perpendicular to the allyl group, as indicated by the N—N—C—C torsion angle of 79.2 (3)°. In the crystal, the water molecule, lying on a twofold axis, forms O—H⋯N and accepts N—H⋯O hydrogen bonds. Additional C—H⋯O hydrogen bonds contribute to the formation of a chain along the b-axis direction. PMID:24109418
N-(2-Allyl-4-chloro-2H-indazol-5-yl)-4-meth-oxy-benzene-sulfonamide hemi-hydrate.

PubMed

Chicha, Hakima; Kouakou, Assoman; Rakib, El Mostapha; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

The fused five- and six-membered rings in the title compound, C17H16ClN3O3S·0.5H2O, are practically coplanar, with the maximum deviation from the mean plane being 0.057 (3) Å for the C atom bound to the exocyclic N atom. The indazole system makes a dihedral angle of 66.18 (12)° with the plane through the benzene ring, and it is nearly perpendicular to the allyl group, as indicated by the N-N-C-C torsion angle of 79.2 (3)°. In the crystal, the water mol-ecule, lying on a twofold axis, forms O-H⋯N and accepts N-H⋯O hydrogen bonds. Additional C-H⋯O hydrogen bonds contribute to the formation of a chain along the b-axis direction.

Multicanonical molecular dynamics simulations combined with Metadynamics for the free energy landscape of a biomolecular system with high energy barriers

NASA Astrophysics Data System (ADS)

Yonezawa, Yasushige; Shimoyama, Hiromitsu; Nakamura, Haruki

2011-01-01

Multicanonical molecular-dynamics (McMD) simulation and Metadynamics (MetaD) are useful for obtaining the free-energies, and can be mutually complementary. We combined McMD with MetaD, and applied it to the conformational free energy calculations of a proline dipeptide. First, MetaD was performed along the dihedral angle at the prolyl bond and we obtained a coarse biasing potential. After adding the biasing potential to the dihedral angle potential energy, we conducted McMD with the modified potential energy. Enhanced sampling was achieved for all degrees-of-freedom, and the sampling of the dihedral angle space was facilitated. After reweighting, we obtained an accurate free energy landscape.
We are Family: the Conformations of 1-FLUOROALKANES, C_nH2n+1F (n = 2,3,4,5,6,7,8)

NASA Astrophysics Data System (ADS)

Obenchain, Daniel A.; Orellana, W.; Cooke, S. A.

2016-06-01

he pure rotational spectra of the n = 5, 6, 7, and 8 members of the 1-fluoroalkane family have been recorded between 7 GHz and 14 GHz using chirped pulse Fourier transform microwave spectroscopy. The spectra have been analyzed and results will be presented and compared with previous work on the n= 2, 3, and 4 members. The lowest energy conformer for all family members has the common feature that the fluorine is in a gauche position relative to the alkyl tail for which all other heavy atom dihedral angles, where appropriate, are 180 degrees. For the n = 3 and higher family members the second lowest energy conformer has all heavy atom dihedral angles equal to 180 degrees. For each family member transitions carried by both low energy conformers were observed in the collected rotational spectra. Quantum chemical calculations were performed and trends in the energy separations between these two common conformers will be presented as a function of chain length. Furthermore, longer chain lengths have been examined using only quantum chemical calculations and results will be presented. M. Hayashi, M. Fujitake, T. Inagusa, S. Miyazaki, J.Mol.Struct., 216, 9-26, 1990 W. Caminati, A. C. Fantoni, F. Manescalchi, F. Scappini, Mol.Phys., 64, 1089 ,1988 L. B. Favero, A. Maris, A. Degli Esposti, P. G. Favero, W. Caminati, G. Pawelke, Chem.Eur.J., 6(16), 3018-3025, 2000
1-Dodecylindoline-2,3-dione

PubMed Central

Qachchachi, Fatima-Zahrae; Ouazzani Chahdi, Fouad; Misbahi, Houria; Bodensteiner, Michael; El Ammari, Lahcen

2014-01-01

The structure of the title compound, C20H29NO2, is isotypic to that of its homologue 1-octylindoline-2,3-dione. The indoline ring and the two carbonyl-group O atoms are approximately coplanar, the largest deviation from the mean plane being 0.0760 (10) Å. The mean plane through the fused-ring system is nearly perpendicular to the mean plane passing through the 1-dodecyl chain [dihedral angle = 77.69 (5)°]. All C atoms of the dodecyl group are in an antiperiplanar arrangement. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming a three-dimensional network. PMID:24764928
Tuning the structural and electronic properties of novel thiophene-pyrrole based 1,2,3,4-tetrazine

NASA Astrophysics Data System (ADS)

Dutta, Rakesh; Kalita, Dhruba Jyoti

2017-04-01

Here, we have studied the structural and optoelectronic behaviour of a series of conjugated heterocyclic polymers. The basic monomer unit of the conjugated polymers contains a backbone of novel thiophene and pyrrole based 1,2,3,4-tetrazine. The other oligomers are designed by substituting the basic monomer unit with different electron-donating and electron-withdrawing groups at the nitrogen and the 3rd C-atom of the pyrrole and the thiophene ring respectively. We have calculated dihedral angles, HOMO-LUMO gaps, excitation energies and oscillator strengths by employing TD-DFT method. Our study reveals that compounds having bulky substituents exhibit larger dihedral angles. This in turn renders an increase in the band gaps (ΔH - L). Presence of the electron-withdrawing substituents also increases the ΔH - L values of the oligomers. However, the electron-donating groups decrease the ΔH - L values of the oligomers. Therefore, small electron-donating substituents have an overwhelming effect on the optoelectronic properties of the conjugated polymers which in turn makes them interesting materials with good conduction properties for fabrication of optoelectronic devices such as OLEDs, OFETs and solar cells.
Laser geodynamic satellite thermal/optical/vibrational analysis and testing, volume 2, book 2. [cubes and far fields

NASA Technical Reports Server (NTRS)

1975-01-01

The main tasks described involved an interferometric evaluation of several cubes, a prediction of their dihedral angles, a comparison of these predictions with independent measurements, a prediction and comparison of far field performance, recommendations as to revised dihedral angles and a subsequent analysis of cubes which were reworked to confirm the recommendations. A tolerance study and theoretical evaluation of several cubes was also performed to aid in understanding the results. The far field characteristics evaluated included polarization effects and treated both intensity distribution and encircled energy data. The energy in the 13.2 - 16.9 arc-sec annular region was tabulated as an indicator of performance sensitivity. The results are provided in viewgraph form, and show the average dihedral angle of an original set of test cubes to have been 1.8 arc-sec with an average far field annulus diameter of 18 arc-sec. Since the peak energy in the 13.2 - 16.9 arc-sec annulus was found to occur for a 1.35 arc-sec cube, and since cube tolerances were shown to increase the annulus diameter slightly, a nominal dihedral angle of 1.25 arc-sec was recommended.
Atomic and molecular analysis highlights the biophysics of unprotonated and protonated retinal in UV and scotopic vision.

PubMed

Kubli-Garfias, Carlos; Vázquez-Ramírez, Ricardo; Cabrera-Vivas, Blanca M; Gómez-Reyes, Baldomero; Ramírez, Juan Carlos

2015-09-26

During the photoreaction of rhodopsin, retinal isomerizes, rotating the C11[double bond, length as m-dash]C12 π-bond from cis to an all-trans configuration. Unprotonated (UR) or protonated (PR) retinal in the Schiff's base (SB) is related to UV and light vision. Because the UR and PR have important differences in their physicochemical reactivities, we compared the atomic and molecular properties of these molecules using DFT calculations. The C10-C11[double bond, length as m-dash]C12-C13 dihedral angle was rotated from 0° to 180° in 45° steps, giving five conformers, and the following were calculated from them: atomic orbital (AO) contributions to the HOMO and LUMO, atomic charges, bond length, bond order, HOMO, LUMO, hardness, electronegativity, polarizability, electrostatic potential, UV-vis spectra and dipole moment (DM). Similarly, the following were analyzed: the energy profile, hybridization, pyramidalization and the hydrogen-out-of-plane (HOOP) wagging from the H11-C11[double bond, length as m-dash]C12-H12 dihedral angle. In addition, retinal with a water H-bond (HR) in the SB was included for comparison. Interestingly, in the PR, C11 and C12 are totally the LUMO and the HOMO, respectively, and have a large electronegativity difference, which predicts an electron jump in these atoms during photoexcitation. At the same time, the PR showed a longer bond length and lower bond order, with a larger DM, lower HOMO-LUMO gap, lower hardness and higher electronegativity. In addition, the AOs of -45° and -90° conformers changed significantly, from pz to py, during the rotation concomitantly with marked hybridization, smooth pyramidalization and lower HOOP activity. Clearly, the atomic and molecular differences between the UR and PR are overwhelming, including the rotational energy profile and light absorption spectra, which indicates that light absorption of UR and PR is already determined by the retinal characteristics of the SB protonation. The HR-model compared with UR shows a lower energy barrier and a discreet bathochromic effect in the UV region.
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
2-Ferrocenyl-6-methylpyridin-3-ol

PubMed Central

Wang, Zhi-Qiang; Xu, Chen; Cen, Fei-Fei; Li, Ying-Fei; Ji, Bao-Ming

2008-01-01

In the title compound, [Fe(C5H5)(C11H10NO)], the dihedral angle between the pyridyl and substituted cyclopentadienyl rings is 20.4 (3)°. The H atoms of the methyl group are disordered over two positions; their site-occupation factors were fixed at 0.5. The crystal structure is stabilized by well defined intermolecular O—H⋯N and C—H⋯O hydrogen bonds, leading to the formation of a two-dimensional network parallel to (101). PMID:21581222
Stereochemical model for proflavin intercalation in A-DNA.

PubMed Central

Alden, C J; Arnott, S

1977-01-01

Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming trans, with all sugars retaining the characteristics C3'-endo pucker. This extended conformation results in virtually no helical unwinding, suggesting it may be an appropriate model for an intercalative intermediary in mutagenesis by virtue of its similarity to standard helical DNA. PMID:593890
(2E)-1-(2,6-Dichloro-3-fluoro-phen-yl)-3-phenyl-prop-2-en-1-one.

PubMed

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

2012-04-01

In the title compound, C(15)H(9)Cl(2)FO, the F atom shows positional disorder over two positions, with site-occupancy factors of 0.747 (4) and 0.253 (4). The dihedral angle between the rings is 86.37 (10)°. In the crystal, C-H⋯O contacts connect the mol-ecules into chains along the c axis. The shortest inter-centroid distance between two aromatic systems is 3.6686 (12) Å and is apparent between the halogenated rings.
Fluid Distribution in Synthetic Wet Halite Rocks : Inference from Measured Elastic Wave Velocity and Electrical Conductivity

NASA Astrophysics Data System (ADS)

Watanabe, T.; Kitano, M.

2011-12-01

Intercrystalline fluid can significantly affect rheological and transport properties of rocks. Its influences are strongly dependent on its distribution. The dihedral angle between solid and liquid phases has been widely accepted as a key parameter that controls solid-liquid textures. The liquid phase is not expected to be interconnected if the dihedral angle is larger than 60 degree. However, observations contradictory to dihedral angle values have been reported. Watanabe (2010) suggested the coexistence of grain boundary fluid with a positive dihedral angle. For good understanding of fluid distribution, it is thus critical to study the nature of grain boundary fluid. We have developed a high pressure and temperature apparatus for study of intercrystalline fluid distribution. It was specially designed for measurements of elastic wave velocities and electrical conductivity. The apparatus mainly consists of a conventional cold-seal vessel with an external heater. The pressure medium is silicon oil of the viscosity of 0.1 Pa s. The pressure and temperature can be controlled from 0 to 200 MPa and from 20 to 200 C, respectively. Dimensions of a sample are 9 mm in diameter, and 15 mm in length. Halite-water system is used as an analog for crustal rocks. The dihedral angle has been studied systematically at various pressure and temperature conditions [Lewis and Holness, 1996]. The dihedral angle is larger than 60 degree at lower pressure and temperature. It decreases to be smaller than 60 degree with increasing pressure and temperature. A sample is prepared by cold-pressing and annealing of wet NaCl powder. Optical examination has shown that synthesized samples are microstructurally homogeneous. Grains are polygonal and equidimensional with a mean diameter of 100 micrometer. Grain boundaries vary from straight to bowed and 120 degree triple junctions are common. Gas and fluid bearing inclusions are visible on the grain boundaries. There are spherical inclusions or isolated worm-like channels. In this presentation, we will report preliminary results of compressional wave velocity and electrical conductivity measurements.
Tuning cofactor redox potentials: the 2-methoxy dihedral angle generates a redox potential difference of >160 mV between the primary (Q(A)) and secondary (Q(B)) quinones of the bacterial photosynthetic reaction center.

PubMed

Taguchi, Alexander T; Mattis, Aidas J; O'Malley, Patrick J; Dikanov, Sergei A; Wraight, Colin A

2013-10-15

Only quinones with a 2-methoxy group can act simultaneously as the primary (QA) and secondary (QB) electron acceptors in photosynthetic reaction centers from Rhodobacter sphaeroides. (13)C hyperfine sublevel correlation measurements of the 2-methoxy in the semiquinone states, SQA and SQB, were compared with quantum mechanics calculations of the (13)C couplings as a function of the dihedral angle. X-ray structures support dihedral angle assignments corresponding to a redox potential gap (ΔEm) between QA and QB of ~180 mV. This is consistent with the failure of a ubiquinone analogue lacking the 2-methoxy to function as QB in mutant reaction centers with a ΔEm of ≈160-195 mV.
Methyl 6-eth-oxy-3-phenyl-3a,4-dihydro-3H-chromeno[4,3-c]isoxazole-3a-car-boxylate.

PubMed

Suresh, G; Srinivasan, J; Bakthadoss, M; Aravindhan, S

2013-02-01

In the title compound, C(20)H(19)NO(5), the dihedral angle between the mean plane of the pyran ring (which has a half-chair conformation) and the benzene ring of the chromeno ring system is 7.21 (7)°. The dihedral angle between the mean plane of the chromeno ring system and the isoxazole ring is 21.78 (6)°, while the isoxazole ring forms a dihedral angle of 72.60 (8)° with the attached phenyl ring. In the crystal, mol-ecules are linked via pairs of C-H⋯O hydrogen bonds, forming inversion dimers with an R(2) (2)(10) ring motif. These dimers are linked via C-H⋯N hydrogen bonds, forming chains along [001].
Butane dihedral angle dynamics in water is dominated by internal friction

PubMed Central

Daldrop, Jan O.; Kappler, Julian; Brünig, Florian N.; Netz, Roland R.

2018-01-01

The dihedral dynamics of butane in water is known to be rather insensitive to the water viscosity; possible explanations for this involve inertial effects or Kramers’ turnover, the finite memory time of friction, and the presence of so-called internal friction. To disentangle these factors, we introduce a method to directly extract the friction memory function from unconstrained simulations in the presence of an arbitrary free-energy landscape. By analysis of the dihedral friction in butane for varying water viscosity, we demonstrate the existence of an internal friction contribution that does not scale linearly with water viscosity. At normal water viscosity, the internal friction turns out to be eight times larger than the solvent friction and thus completely dominates the effective friction. By comparison with simulations of a constrained butane molecule that has the dihedral as the only degree of freedom, we show that internal friction comes from the six additional degrees of freedom in unconstrained butane that are orthogonal to the dihedral angle reaction coordinate. While the insensitivity of butane’s dihedral dynamics to water viscosity is solely due to the presence of internal friction, inertial effects nevertheless crucially influence the resultant transition rates. In contrast, non-Markovian effects due to the finite memory time are present but do not significantly influence the dihedral barrier-crossing rate of butane. These results not only settle the character of dihedral dynamics in small solvated molecular systems such as butane, they also have important implications for the folding of polymers and proteins. PMID:29712838
DOE Office of Scientific and Technical Information (OSTI.GOV)

N, Rekha T.; Rajkumar, Beulah J. M., E-mail: beulah-rajkumar@yahoo.co.in

Charge transfer properties of pentacene adsorbed on silver is investigated using DFT methods. Optimized geometry of pentacene after adsorption on silver indicates distortion in hexagonal structure of the ring close to the silver cluster and deviations in co-planarity of carbon atoms due to the variations in bond angles and dihedral angles. Theoretically simulated absorption spectrum has a symmetric surface plasmon resonance peak around 486nm corresponding to the transfer of charge from HOMO-2 to LUMO. Theoretical SERS confirms the process of adsorption, tilted orientation of pentacene on silver surface and the charge transfers reported. Localization of electron density arising from redistributionmore » of electrostatic potential together with a reduced bandgap of pentacene after adsorption on silver suggests its utility in the design of electro active organic semiconducting devices.« less
5-Bromo-N-methylpyrimidin-2-amine

PubMed Central

Yang, Qi; Xu, Ning; Zhu, Kai; Lv, Xiaoping; Han, Ping-fang

2012-01-01

In the title molecule, C5H6BrN3, the pyrimidine ring is essentially planar, with an r.m.s. deviation of 0.007 Å. The Br and N atoms substituted to the pyrimidine ring are coplanar with the ring [displacements = 0.032 (1) and 0.009 (5) Å, respectively], while the methyl C atom lies 0.100 (15) Å from this plane with a dihedral angle between the pyrimidine ring and the methylamine group of 4.5 (3)°. In the crystal, C—H⋯N, C—H⋯Br and N—H⋯N hydrogen bonds link the molecules into a two-dimensional network in the (011) plane. PMID:22259398
Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.
Crystal structure of 2-((1E)-{2-[bis-(2-methyl-benzyl-sulfan-yl)methyl-idene]hydrazin-1-yl-idene}meth-yl)-6-meth-oxy-phenol.

PubMed

Yusof, Enis Nadia Md; Ravoof, Thahira Begum S A; Tahir, Mohamed Ibrahim Mohamed; Tiekink, Edward R T

2015-04-01

In the title compound, C25H26N2O2S2, the central CN2S2 atoms are almost coplanar (r.m.s. deviation = 0.0058 Å). One phenyl ring clearly lies to one side of the central plane, while the other is oriented in the plane but splayed. Despite the different relative orientations, the phenyl rings form similar dihedral angles of 64.90 (3) and 70.06 (3)° with the central plane, and 63.28 (4)° with each other. The benzene ring is twisted with respect to the central plane, forming a dihedral angle of 13.17 (7)°. The S2C=N, N-N and N-N=C bond lengths of 1.2919 (19), 1.4037 (17) and 1.2892 (19) Å, respectively, suggest limited conjugation over these atoms; the configuration about the N-N=C bond is E. An intra-molecular O-H⋯N hydrogen bond is noted. In the crystal, phen-yl-meth-oxy C-H⋯O and phen-yl-phenyl C-H⋯π inter-actions lead to supra-molecular double chains parallel to the b axis. These are connected into a layer via meth-yl-phenyl C-H⋯π inter-actions, and layers stack along the a axis, being connected by weak π-π inter-actions between phenyl rings [inter-centroid distance = 3.9915 (9) Å] so that a three-dimensional architecture ensues.
A 2:1 co-crystal of p-nitro-benzoic acid and N,N'-bis-(pyridin-3-ylmeth-yl)ethanedi-amide: crystal structure and Hirshfeld surface analysis.

PubMed

Syed, Sabrina; Halim, Siti Nadiah Abdul; Jotani, Mukesh M; Tiekink, Edward R T

2016-01-01

The title 2:1 co-crystal, 2C7H5NO4·C14H14N4O2, in which the complete di-amide mol-ecule is generated by crystallographic inversion symmetry, features a three-mol-ecule aggregate sustained by hydroxyl-O-H⋯N(pyrid-yl) hydrogen bonds. The p-nitro-benzoic acid mol-ecule is non-planar, exhibiting twists of both the carb-oxy-lic acid and nitro groups, which form dihedral angles of 10.16 (9) and 4.24 (4)°, respectively, with the benzene ring. The di-amide mol-ecule has a conformation approximating to a Z shape, with the pyridyl rings lying to either side of the central, almost planar di-amide residue (r.m.s. deviation of the eight atoms being 0.025 Å), and forming dihedral angles of 77.22 (6)° with it. In the crystal, three-mol-ecule aggregates are linked into a linear supra-molecular ladder sustained by amide-N-H⋯O(nitro) hydrogen bonds and orientated along [10-4]. The ladders are connected into a double layer via pyridyl- and benzene-C-H⋯O(amide) inter-actions, which, in turn, are connected into a three-dimensional architecture via π-π stacking inter-actions between pyridyl and benzene rings [inter-centroid distance = 3.6947 (8) Å]. An evaluation of the Hirshfeld surfaces confirm the importance of inter-molecular inter-actions involving oxygen atoms as well as the π-π inter-actions.
Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping.

PubMed

Frickenhaus, Stephan; Kannan, Srinivasaraghavan; Zacharias, Martin

2009-02-01

A direct conformational clustering and mapping approach for peptide conformations based on backbone dihedral angles has been developed and applied to compare conformational sampling of Met-enkephalin using two molecular dynamics (MD) methods. Efficient clustering in dihedrals has been achieved by evaluating all combinations resulting from independent clustering of each dihedral angle distribution, thus resolving all conformational substates. In contrast, Cartesian clustering was unable to accurately distinguish between all substates. Projection of clusters on dihedral principal component (PCA) subspaces did not result in efficient separation of highly populated clusters. However, representation in a nonlinear metric by Sammon mapping was able to separate well the 48 highest populated clusters in just two dimensions. In addition, this approach also allowed us to visualize the transition frequencies between clusters efficiently. Significantly, higher transition frequencies between more distinct conformational substates were found for a recently developed biasing-potential replica exchange MD simulation method allowing faster sampling of possible substates compared to conventional MD simulations. Although the number of theoretically possible clusters grows exponentially with peptide length, in practice, the number of clusters is only limited by the sampling size (typically much smaller), and therefore the method is well suited also for large systems. The approach could be useful to rapidly and accurately evaluate conformational sampling during MD simulations, to compare different sampling strategies and eventually to detect kinetic bottlenecks in folding pathways.

High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy

NASA Astrophysics Data System (ADS)

Jaroniec, Christopher P.; Macphee, Cait E.; Bajaj, Vikram S.; McMahon, Michael T.; Dobson, Christopher M.; Griffin, Robert G.

2004-01-01

Amyloid fibrils are self-assembled filamentous structures associated with protein deposition conditions including Alzheimer's disease and the transmissible spongiform encephalopathies. Despite the immense medical importance of amyloid fibrils, no atomic-resolution structures are available for these materials, because the intact fibrils are insoluble and do not form diffraction-quality 3D crystals. Here we report the high-resolution structure of a peptide fragment of the amyloidogenic protein transthyretin, TTR(105-115), in its fibrillar form, determined by magic angle spinning NMR spectroscopy. The structure resolves not only the backbone fold but also the precise conformation of the side chains. Nearly complete 13C and 15N resonance assignments for TTR(105-115) formed the basis for the extraction of a set of distance and dihedral angle restraints. A total of 76 self-consistent experimental measurements, including 41 restraints on 19 backbone dihedral angles and 35 13C-15N distances between 3 and 6 Å were obtained from 2D and 3D NMR spectra recorded on three fibril samples uniformly 13C, 15N-labeled in consecutive stretches of four amino acids and used to calculate an ensemble of peptide structures. Our results indicate that TTR(105-115) adopts an extended -strand conformation in the amyloid fibrils such that both the main- and side-chain torsion angles are close to their optimal values. Moreover, the structure of this peptide in the fibrillar form has a degree of long-range order that is generally associated only with crystalline materials. These findings provide an explanation of the unusual stability and characteristic properties of this form of polypeptide assembly.
Butane dihedral angle dynamics in water is dominated by internal friction.

PubMed

Daldrop, Jan O; Kappler, Julian; Brünig, Florian N; Netz, Roland R

2018-05-15

The dihedral dynamics of butane in water is known to be rather insensitive to the water viscosity; possible explanations for this involve inertial effects or Kramers' turnover, the finite memory time of friction, and the presence of so-called internal friction. To disentangle these factors, we introduce a method to directly extract the friction memory function from unconstrained simulations in the presence of an arbitrary free-energy landscape. By analysis of the dihedral friction in butane for varying water viscosity, we demonstrate the existence of an internal friction contribution that does not scale linearly with water viscosity. At normal water viscosity, the internal friction turns out to be eight times larger than the solvent friction and thus completely dominates the effective friction. By comparison with simulations of a constrained butane molecule that has the dihedral as the only degree of freedom, we show that internal friction comes from the six additional degrees of freedom in unconstrained butane that are orthogonal to the dihedral angle reaction coordinate. While the insensitivity of butane's dihedral dynamics to water viscosity is solely due to the presence of internal friction, inertial effects nevertheless crucially influence the resultant transition rates. In contrast, non-Markovian effects due to the finite memory time are present but do not significantly influence the dihedral barrier-crossing rate of butane. These results not only settle the character of dihedral dynamics in small solvated molecular systems such as butane, they also have important implications for the folding of polymers and proteins. Copyright © 2018 the Author(s). Published by PNAS.
Contact- and distance-based principal component analysis of protein dynamics.

PubMed

Ernst, Matthias; Sittel, Florian; Stock, Gerhard

2015-12-28

To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal coordinates, e.g., backbone dihedral angles or various kinds of distances, may be used as input data in a PCA. Adopting two well-known model problems, folding of villin headpiece and the functional dynamics of BPTI, a systematic study of PCA using distance-based measures is presented which employs distances between Cα-atoms as well as distances between inter-residue contacts including side chains. While this approach seems prohibitive for larger systems due to the quadratic scaling of the number of distances with the size of the molecule, it is shown that it is sufficient (and sometimes even better) to include only relatively few selected distances in the analysis. The quality of the PCA is assessed by considering the resolution of the resulting free energy landscape (to identify metastable conformational states and barriers) and the decay behavior of the corresponding autocorrelation functions (to test the time scale separation of the PCA). By comparing results obtained with distance-based, dihedral angle, and Cartesian coordinates, the study shows that the choice of input variables may drastically influence the outcome of a PCA.
Contact- and distance-based principal component analysis of protein dynamics

NASA Astrophysics Data System (ADS)

Ernst, Matthias; Sittel, Florian; Stock, Gerhard

2015-12-01

To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal coordinates, e.g., backbone dihedral angles or various kinds of distances, may be used as input data in a PCA. Adopting two well-known model problems, folding of villin headpiece and the functional dynamics of BPTI, a systematic study of PCA using distance-based measures is presented which employs distances between Cα-atoms as well as distances between inter-residue contacts including side chains. While this approach seems prohibitive for larger systems due to the quadratic scaling of the number of distances with the size of the molecule, it is shown that it is sufficient (and sometimes even better) to include only relatively few selected distances in the analysis. The quality of the PCA is assessed by considering the resolution of the resulting free energy landscape (to identify metastable conformational states and barriers) and the decay behavior of the corresponding autocorrelation functions (to test the time scale separation of the PCA). By comparing results obtained with distance-based, dihedral angle, and Cartesian coordinates, the study shows that the choice of input variables may drastically influence the outcome of a PCA.
4-[(1-Benzyl-1H-1,2,3-triazol-4-yl)meth-oxy]benzene-1,2-dicarbo-nitrile: crystal structure, Hirshfeld surface analysis and energy-minimization calculations.

PubMed

Shamsudin, Norzianah; Tan, Ai Ling; Young, David J; Jotani, Mukesh M; Otero-de-la-Roza, A; Tiekink, Edward R T

2016-04-01

In the solid state, the title compound, C18H13N5O, adopts a conformation whereby the phenyl ring and meth-oxy-benzene-1,2-dicarbo-nitrile residue (r.m.s. deviation of the 12 non-H atoms = 0.041 Å) lie to opposite sides of the central triazolyl ring, forming dihedral angles of 79.30 (13) and 64.59 (10)°, respectively; the dihedral angle between the outer rings is 14.88 (9)°. This conformation is nearly 7 kcal mol(-1) higher in energy than the energy-minimized structure which has a syn disposition of the outer rings, enabling intra-molecular π-π inter-actions. In the crystal, methyl-ene-C-H⋯N(triazol-yl) and carbo-nitrile-N⋯π(benzene) inter-actions lead to supra-molecular chains along the a axis. Supra-molecular layers in the ab plane arise as the chains are connected by benzene-C-H⋯N(carbo-nitrile) inter-actions; layers stack with no directional inter-actions between them. The specified inter-molecular contacts along with other, weaker contributions to the supra-molecular stabilization are analysed in a Hirshfeld surface analysis.
A simple molecular mechanics integrator in mixed rigid body and dihedral angle space

PubMed Central

Vitalis, Andreas; Pappu, Rohit V.

2014-01-01

We propose a numerical scheme to integrate equations of motion in a mixed space of rigid-body and dihedral angle coordinates. The focus of the presentation is biomolecular systems and the framework is applicable to polymers with tree-like topology. By approximating the effective mass matrix as diagonal and lumping all bias torques into the time dependencies of the diagonal elements, we take advantage of the formal decoupling of individual equations of motion. We impose energy conservation independently for every degree of freedom and this is used to derive a numerical integration scheme. The cost of all auxiliary operations is linear in the number of atoms. By coupling the scheme to one of two popular thermostats, we extend the method to sample constant temperature ensembles. We demonstrate that the integrator of choice yields satisfactory stability and is free of mass-metric tensor artifacts, which is expected by construction of the algorithm. Two fundamentally different systems, viz., liquid water and an α-helical peptide in a continuum solvent are used to establish the applicability of our method to a wide range of problems. The resultant constant temperature ensembles are shown to be thermodynamically accurate. The latter relies on detailed, quantitative comparisons to data from reference sampling schemes operating on exactly the same sets of degrees of freedom. PMID:25053299
2,2′-Bi(9,9-diethylfluorene)

PubMed Central

Park, Ki-Min; Oh, Hankook; Kang, Youngjin

2014-01-01

The title compound, C34H34, systematic name 9,9,9′,9′-tetraethyl-2,2′-bi(9H-fluorene), crystallized with two crystallographically independent molecules (A and B) in the asymmetric unit. These differ mainly in the orientation of the lateral ethyl chains: in molecule A, they are both on the same side of the molecule whereas in molecule B, one diethylfluorene moiety has undergone a 180° rotation such that the two pairs of ethyl residues appear on opposite sides of the molecule. The fluorene ring systems subtend dihedral angles of 31.37 (4) and 43.18 (3)° in molecules A and B, respectively. Hence the two fluorene moieties are tilted slightly toward one another. This may be due to the presence of intermolecular C—H⋯π interactions between neighboring molecules. The lateral ethyl chains (excluding H atoms) are also almost planar, with each pair almost perpendicular to the plane of the fluorene system to which they are attached with dihedral angles between the ethyl and fluorene planes in the range 86.04 (8)–89.5 (1)°. PMID:24764898
Crystal structure of 2-meth-oxy-2-[(4-meth-oxy-phen-yl)sulfan-yl]-1-phenyl-ethanone.

PubMed

Caracelli, Ignez; Olivato, Paulo R; Traesel, Henrique J; Valença, Jéssica; Rodrigues, Daniel N S; Tiekink, Edward R T

2015-09-01

In the title β-thio-carbonyl compound, C16H16O3S, the adjacent meth-oxy and carbonyl O atoms are synperiplanar [the O-C-C-O torsion angle is 19.8 (4)°] and are separated by 2.582 (3) Å. The dihedral angle between the rings is 40.11 (16)°, and the meth-oxy group is coplanar with the benzene ring to which it is connected [the C-C-O-C torsion angle is 179.1 (3)°]. The most notable feature of the crystal packing is the formation of methine and methyl C-H⋯O(carbon-yl) inter-actions that lead to a supra-molecular chain with a zigzag topology along the c axis. Chains pack with no specific inter-molecular inter-actions between them.
4-[(E)-(2,4-Difluoro-phen-yl)(hydroxy-imino)meth-yl]piperidinium picrate.

PubMed

Jasinski, Jerry P; Butcher, Ray J; Yathirajan, H S; Mallesha, L; Mohana, K N

2009-09-05

The title compound, C(12)H(15)F(2)N(2)O(+)·C(6)H(2)N(3)O(7) (-), a picrate salt of 4-[(E)-(2,4-difluoro-phen-yl)(hydroxy-imino)meth-yl]piper-idine, crystallizes with two independent mol-ecules in a cation-anion pair in the asymmetric unit. In the cation, a methyl group is tris-ubstituted by hydroxy-imino, piperidin-4-yl and 2,4-difluoro-phenyl groups, the latter of which contains an F atom disordered over two positions in the ring [occupancy ratio 0.631 (4):0.369 (4)]. The mean plane of the hydr-oxy group is in a synclinical conformation nearly orthogonal [N-C-C-C = 72.44 (19)°] to the mean plane of the piperidine ring, which adopts a slightly distorted chair conformation. The dihedral angle between the mean plane of the 2,4-difluoro-phenyl and piperidin-4-yl groups is 60.2 (3)°. In the picrate anion, the mean planes of the two o-NO(2) and single p-NO(2) groups adopt twist angles of 5.7 (2), 25.3 (7) and 8.3 (6)°, respectively, with the attached planar benzene ring. The dihedral angle between the mean planes of the benzene ring in the picrate anion and those in the hydroxy-imino, piperidin-4-yl and 2,4-difluoro-phenyl groups in the cation are 84.9 (7), 78.9 (4) and 65.1 (1)°, respectively. Extensive hydrogen-bond inter-actions occur between the cation-anion pair, which help to establish the crystal packing in the unit cell. This includes dual three-center hydrogen bonds with the piperidin-4-yl group, the phenolate and o-NO(2) O atoms of the picrate anion at different positions in the unit cell, which form separate N-H⋯(O,O) bifurcated inter-molecular hydrogen-bond inter-actions. Also, the hydr-oxy group forms a separate hydrogen bond with a nearby piperidin-4-yl N atom, thus providing two groups of hydrogen bonds, which form an infinite two-dimensional network along (011).
The gamut of alkoxy radicals

NASA Astrophysics Data System (ADS)

Box, Harold C.; Budzinski, Edwin E.; Freund, Harold G.

1984-12-01

It is shown that various radicals exhibiting diverse ESR and ENDOR spectral characteristics are nonetheless a closely related family of alkoxy radicals. The relationship is established by correlating the g tensor with crystal structure and by relating dihedral angles inferred from proton hyperfine couplings to dihedral angles inferred from the g tensor and crystal structure. The analysis also serves to demonstrate that an ESR absorption observed in x-irradiated single crystals of uridine 5'-monophosphate is due to an alkoxy radical.
3-(4-Carboxy-5-carboxylato-1H-imidazol-2-yl)pyridin-1-ium monohydrate

PubMed Central

Liu, Guang-Jun; Zhao, Guang-Wang; Li, Li; Gao, Hong-Tao

2011-01-01

In the zwitterionic molecule of the title compound, C10H7N3O4·H2O, one carboxyl group is deprotonated and the pyridine N atom is protonated. The pyridinium and imidazole rings form a dihedral angle of 5.23 (1)°. An intramolecular O—H⋯O hydrogen bond occurs. In the crystal, intermolecular N—H⋯O, O—H⋯N and O—H⋯O hydrogen bonds link the zwitterions and water molecules into sheets parallel to (102). PMID:21523144
1,4-Bis(4H-1,2,4-triazol-4-yl)benzene dihydrate

PubMed Central

Wang, Xiu-Guang; Li, Jian-Hui; Ding, Bin; Du, Gui-Xiang

2012-01-01

The asymmetric unit of the title compound, C10H8N6·2H2O, comprises half the organic species, the molecule being completed by inversion symmetry, and one water molecule. The dihedral angle between the 1,2,4-triazole ring and the central benzene ring is 32.2 (2)°. The water molecules form O—H⋯N hydrogen bonds with N-atom acceptors of the triazole rings. C—H⋯N hydrogen bonds are also observed, giving a three-dimensional framework. PMID:22904851
N-[4-Cyano-3-(trifluoromethyl)phenyl]-2-ethoxybenzamide

PubMed Central

Naveen, S.; Basappa; Manjunath, H. R.; Sridhar, M. A.; Shashidhara Prasad, J.; Rangappa, K. S.

2010-01-01

In the title compound, C17H13F3N2O2, the two aromatic rings are essentially coplanar, forming a dihedral angle of 2.78 (12)°. The non-H atoms of the ethoxy group are coplanar with the attached ring [maximum deviation = 0.271 (3) Å]. An intramolecular N—H⋯O hydrogen bond occurs. In the crystal structure, molecules are linked by intermolecular C—H⋯N and C—H⋯F hydrogen bonds. PMID:21587782
6-Oxo-5-[(trifluoromethyl)sulfonyl]-1,2,4a,5,6,11b-hexahydro-1,3-dioxolo[4,5-j]phenanthridin-2-yl benzoate

PubMed Central

Wu, Chunli; Li, Pan; Shi, Xiufang; Pan, Xiaotao; Wu, Jizhou

2011-01-01

In the title compound, C22H16F3NO7S, the two benzene rings are almost perpendicular, the dihedral angle between their mean planes being 87.1 (1)°. The terminal O atom of the benzoate moiety is disordered over two positions with site occupancies of 0.244 (15) and 0.756 (15). The crystal structure is stablized by two types of weak intermolecular C—H⋯O hydrogen bonds. PMID:21523058
1,3-Bis[(5-amino-furan-2-yl)meth-yl]-3,4,5,6-tetra-hydro-pyrimidin-1-ium hexa-fluoro-phosphate.

PubMed

Akkurt, Mehmet; Akkoç, Senem; Gök, Yetkin; Tahir, Muhammad Nawaz

2013-01-01

The asymmetric unit of the title salt, C16H21N2O2 (+)·PF6 (-), contains half of the whole ion pair, which has crystallographic mirror symmetry. Two F atoms related by the mirror plane are disordered over two sites of equal occupancy. The dihedral angle between the central ring and the furan ring is 59.3 ()°. In the crystal, the anions and cations are linked through C-H⋯F inter-actions, forming a three-dimensional network.
Crystal structure of N-(3-chloro-1-methyl-1H-indazol-5-yl)-4-meth-oxy-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Gamouh, Ahmed; Saadi, Mohamed; El Ammari, Lahcen

2014-09-01

In the title compound, C15H14ClN3O3S, the dihedral angle between the planes of the indazole ring system (r.m.s. deviation = 0.007 Å) and the benzene ring is 89.05 (7)°. The meth-oxy C atom deviates from its attached ring by 0.196 (3) Å. In the crystal, inversion dimers linked by pairs of N-H⋯O hydrogen bonds generate R 2 (2)(8) loops. The dimers are connected into [010] chains by C-H⋯O inter-actions.
2-(2-Thienyl)-4,5-dihydro-1H-imidazole

PubMed Central

Kia, Reza; Fun, Hoong-Kun; Kargar, Hadi

2009-01-01

In title compound, C7H8N2S, the five-membered rings are twisted by a dihedral angle of 5.17 (10)°. Two intermolecular N—H⋯N and C—H⋯N hydrogen bonds to the same acceptor N atom form seven-membered rings, producing R 2 1(7) ring motifs. These interactions link neighbouring molecules into one-dimensional chains extended along the c axis. The crystal structure is further stabilized by weak intermolecular C—H⋯π interactions. PMID:21581910
4-(4-Bromo-phen-yl)-1-(2,6-difluoro-benz-yl)-3-(3,4,5-trimeth-oxy-phen-yl)-1H-1,2,4-triazole-5(4H)-thione.

PubMed

Fun, Hoong-Kun; Ooi, Chin Wei; Chandrakantha, B; Isloor, Arun M; Shetty, Prakash

2012-01-01

In the title compound, C(24)H(20)BrF(2)N(3)O(3)S, the triazole ring (r.m.s. deviation = 0.0107 Å) makes dihedral angles of 28.18 (14), 63.76 (14) and 77.01 (18)°, respectively, with the trimeth-oxy-, bromo-, and difluoro-substituted benzene rings. The C atoms of the meta meth-oxy groups are roughly coplanar with their ring [displacements = -0.289 (4) and 0.083 (7) Å], whereas the C atom of the para group is displaced [1.117 (3) Å]. In the crystal, inversion dimers linked by two pairs of C-H⋯O hydrogen bonds occur. The ring motif of the two hydrogen bonds to their symmetry-generated O-atom acceptors is R(2) (2)(8).
2-(4,5-Dihydro-1H-imidazol-2-yl)pyridine

PubMed Central

Kia, Reza; Fun, Hoong-Kun; Kargar, Hadi

2009-01-01

In the molecule of the title compound, C8H9N3, a new imidazoline derivative, the six- and five-membered rings are slightly twisted away from each other, forming a dihedral angle of 7.96 (15)°. In the crystal structure, neighbouring molecules are linked together by intermolecular N—H⋯N hydrogen bonds into extended one-dimensional chains along the a axis. The pyridine N atom is in close proximity to a carbon-bound H atom of the imidazoline ring, with an H⋯N distance of 2.70 Å, which is slightly shorter than the sum of the van der Waals radii of these atoms (2.75 Å). The crystal structure is further stabilized by intermolecular C—H⋯π and π–π interactions (centroid-to-centroid distance 3.853 Å). PMID:21582505
(Carbonato-κO,O')bis-(di-2-pyridyl-amine-κN,N')cobalt(III) bromide.

PubMed

Czapik, Agnieszka; Papadopoulos, Christos; Lalia-Kantouri, Maria; Gdaniec, Maria

2011-04-01

In the title compound, [Co(CO(3))(C(10)H(9)N(3))(2)]Br, a distorted octa-hedral coordination of the Co(III) atom is completed by four N atoms of the two chelating di-2-pyridyl-amine ligands and two O atoms of the chelating carbonate anion. The di-2-pyridyl-amine ligands are nonplanar and the dihedral angles between the 2-pyridyl groups are 29.11 (9) and 37.15 (12)°. The coordination cation, which has approximate C(2) symmetry, is connected to the bromide ion via an N-H⋯Br(-) hydrogen bond. The ionic pair thus formed is further assembled into a dimer via N-H⋯O inter-actions about an inversion centre. A set of weaker C-H⋯O and C-H⋯Br(-) inter-actions connect the dimers into a three-dimensional network.

(Carbonato-κ2 O,O′)bis(di-2-pyridylamine-κ2 N,N′)cobalt(III) bromide

PubMed Central

Czapik, Agnieszka; Papadopoulos, Christos; Lalia-Kantouri, Maria; Gdaniec, Maria

2011-01-01

In the title compound, [Co(CO3)(C10H9N3)2]Br, a distorted octahedral coordination of the CoIII atom is completed by four N atoms of the two chelating di-2-pyridylamine ligands and two O atoms of the chelating carbonate anion. The di-2-pyridylamine ligands are nonplanar and the dihedral angles between the 2-pyridyl groups are 29.11 (9) and 37.15 (12)°. The coordination cation, which has approximate C 2 symmetry, is connected to the bromide ion via an N—H⋯Br− hydrogen bond. The ionic pair thus formed is further assembled into a dimer via N—H⋯O interactions about an inversion centre. A set of weaker C—H⋯O and C—H⋯Br− interactions connect the dimers into a three-dimensional network. PMID:21753946
Charge transfer properties of pentacene adsorbed on silver: DFT study

NASA Astrophysics Data System (ADS)

N, Rekha T.; Rajkumar, Beulah J. M.

2015-06-01

Charge transfer properties of pentacene adsorbed on silver is investigated using DFT methods. Optimized geometry of pentacene after adsorption on silver indicates distortion in hexagonal structure of the ring close to the silver cluster and deviations in co-planarity of carbon atoms due to the variations in bond angles and dihedral angles. Theoretically simulated absorption spectrum has a symmetric surface plasmon resonance peak around 486nm corresponding to the transfer of charge from HOMO-2 to LUMO. Theoretical SERS confirms the process of adsorption, tilted orientation of pentacene on silver surface and the charge transfers reported. Localization of electron density arising from redistribution of electrostatic potential together with a reduced bandgap of pentacene after adsorption on silver suggests its utility in the design of electro active organic semiconducting devices.
An Apparatus for Varying Effective Dihedral in Flight with Application to a Study of Tolerable Dihedral on a Conventional Fighter Airplane

NASA Technical Reports Server (NTRS)

Kauffman, William M; Liddell, Charles J , Jr; Smith, Allan; Van Dyke, Rudolph D , Jr

1949-01-01

An apparatus for varying effective dihedral in flight by means of servo actuation of the ailerons in response to sideslip angle is described. The results of brief flight tests of the apparatus on a conventional fighter airplane are presented and discussed. The apparatus is shown to have satisfactory simulated a wide range of effective dihedral under static and dynamic conditions. The effects of a small amount of servo lag are shown to be measurable when the apparatus is simulating small negative values of dihedral. However, these effects were not considered by the pilots to give the airplane an artificial feel. The results of an investigation employing the apparatus to determine the tolerable (safe for normal fighter operation) range of effective dihedral on the test airplane are presented.
Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation.

PubMed

Echenique, Pablo; Alonso, J L

2006-07-30

A set of rules is defined to systematically number the groups and the atoms of polypeptides in a modular manner. Supported by this numeration, a set of internal coordinates is defined. These coordinates (termed Systematic, Approximately Separable, and Modular Internal Coordinates--SASMIC) are straightforwardly written in Z-matrix form and may be directly implemented in typical Quantum Chemistry packages. A number of Perl scripts that automatically generate the Z-matrix files are provided as supplementary material. The main difference with most Z-matrix-like coordinates normally used in the literature is that normal dihedral angles ("principal dihedrals" in this work) are only used to fix the orientation of whole groups and a different type of dihedrals, termed "phase dihedrals," are used to describe the covalent structure inside the groups. This physical approach allows to approximately separate soft and hard movements of the molecule using only topological information and to directly implement constraints. As an application, we use the coordinates defined and ab initio quantum mechanical calculations to assess the commonly assumed approximation of the free energy, obtained from "integrating out" the side chain degree of freedom chi, by the Potential Energy Surface (PES) in the protected dipeptide HCO-L-Ala-NH2. We also present a subbox of the Hessian matrix in two different sets of coordinates to illustrate the approximate separation of soft and hard movements when the coordinates defined in this work are used. (PACS: 87.14.Ee, 87.15.-v, 87.15.Aa, 87.15.Cc) 2006 Wiley Periodicals, Inc.
View planetary differentiation process through high-resolution 3D imaging

NASA Astrophysics Data System (ADS)

Fei, Y.

2011-12-01

Core-mantle separation is one of the most important processes in planetary evolution, defining the structure and chemical distribution in the planets. Iron-dominated core materials could migrate through silicate mantle to the core by efficient liquid-liquid separation and/or by percolation of liquid metal through solid silicate matrix. We can experimentally simulate these processes to examine the efficiency and time of core formation and its geochemical signatures. The quantitative measure of the efficiency of percolation is usually the dihedral angle, related to the interfacial energies of the liquid and solid phases. To determine the true dihedral angle at high pressure and temperatures, it is necessary to measure the relative frequency distributions of apparent dihedral angles between the quenched liquid metal and silicate grains for each experiment. Here I present a new imaging technique to visualize the distribution of liquid metal in silicate matrix in 3D by combination of focus ion beam (FIB) milling and high-resolution SEM image. The 3D volume rendering provides precise determination of the dihedral angle and quantitative measure of volume fraction and connectivity. I have conducted a series of experiments using mixtures of San Carlos olivine and Fe-S (10wt%S) metal with different metal-silicate ratios, up to 25 GPa and at temperatures above 1800C. High-quality 3D volume renderings were reconstructed from FIB serial sectioning and imaging with 10-nm slice thickness and 14-nm image resolution for each quenched sample. The unprecedented spatial resolution at nano scale allows detailed examination of textural features and precise determination of the dihedral angle as a function of pressure, temperature and composition. The 3D reconstruction also allows direct assessment of connectivity in multi-phase matrix, providing a new way to investigate the efficiency of metal percolation in a real silicate mantle.
Crystal structure of 3-(2,5-di-meth-oxy-phen-yl)propionic acid.

PubMed

Bugenhagen, Bernhard; Al Jasem, Yosef; AlAzani, Mariam; Thiemann, Thies

2015-05-01

In the crystal of the title compound, C11H14O4, the aromatic ring is almost coplanar with the 2-position meth-oxy group with which it subtends a dihedral of 0.54 (2)°, while the 5-position meth-oxy group makes a corresponding dihedral angle of just 5.30 (2)°. The angle between the mean planes of the aromatic ring and the propionic acid group is 78.56 (2)°. The fully extended propionic side chain is in a trans configuration with a C-C-C-C torsion angle of -172.25 (7)°. In the crystal, hydrogen bonding is limited to dimer formation via R 2 (2)(8) rings. The hydrogen-bonded dimers are stacked along the b axis. The average planes of the two benzene rings in a dimer are parallel to each other, but at an offset of 4.31 (2) Å. Within neighbouring dimers along the [101] direction, the average mol-ecular benzene planes are almost perpendicular to each other, with a dihedral angle of 85.33 (2)°.
Atomistic model of the spider silk nanostructure

NASA Astrophysics Data System (ADS)

Keten, Sinan; Buehler, Markus J.

2010-04-01

Spider silk is an ultrastrong and extensible self-assembling biopolymer that outperforms the mechanical characteristics of many synthetic materials including steel. Here we report atomic-level structures that represent aggregates of MaSp1 proteins from the N. Clavipes silk sequence based on a bottom-up computational approach using replica exchange molecular dynamics. We discover that poly-alanine regions predominantly form distinct and orderly beta-sheet crystal domains while disorderly structures are formed by poly-glycine repeats, resembling 31-helices. These could be the molecular source of the large semicrystalline fraction observed in silks, and also form the basis of the so-called "prestretched" molecular configuration. Our structures are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content.
4-Amino-N-(3-methoxypyrazin-2-yl)benzenesulfonamide

PubMed Central

Bruni, Bruno; Coran, Silvia A.; Bartolucci, Gianluca; Di Vaira, Massimo

2010-01-01

The overall molecular geometry of the title compound, C11H12N4O3S, is bent, with a dihedral angle of 89.24 (5)° between the best planes through the two aromatic rings. Each molecule behaves as a hydrogen-bond donor toward three different molecules, through its amidic and the two aminic H atoms, and it behaves as a hydrogen-bond acceptor from two other molecules via one of its sulfonamidic O atoms. In the crystal, molecules linked by N—H⋯N and N—H⋯O hydrogen bonds form kinked layers parallel to (001), adjacent layers being connected by van der Waals interactions. PMID:21587634
Disentangling neighbors and extended range density oscillations in monatomic amorphous semiconductors.

PubMed

Roorda, S; Martin, C; Droui, M; Chicoine, M; Kazimirov, A; Kycia, S

2012-06-22

High energy x-ray diffraction measurements of pure amorphous Ge were made and its radial distribution function (RDF) was determined at high resolution, revealing new information on the atomic structure of amorphous semiconductors. Fine structure in the second peak in the RDF provides evidence that a fraction of third neighbors are closer than some second neighbors; taking this into account leads to a narrow distribution of tetrahedral bond angles, (8.5 ± 0.1)°. A small peak which appears near 5 Å upon thermal annealing shows that some ordering in the dihedral bond-angle distribution takes place during structural relaxation. Extended range order is detected (in both a-Ge and a-Si) which persists to beyond 20 Å, and both the periodicity and its decay length increase upon thermal annealing. Previously, the effect of structural relaxation was only detected at intermediate range, involving reduced tetrahedral bond-angle distortions. These results enhance our understanding of the atomic order in continuous random networks and place significantly more stringent requirements on computer models intending to describe these networks, or their alternatives which attempt to describe the structure in terms of an arrangement of paracrystals.
Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

DTIC Science & Technology

2014-10-01

the angles and dihedrals that are truly unique will be indicated by the user by editing NewAngleTypesDump and NewDihedralTypesDump. The program ...Atomistic Molecular Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Robert M Elder, Timothy W Sirk, and...Antechamber program in Assisted Model Building with Energy Refinement (AMBER) Tools to assign partial charges (using the Austin Model 1 [AM1]-bond charge
N-(3-Chloro-1H-indazol-5-yl)-4-meth-oxy-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Saadi, Mohamed; El Ammari, Lahcen

2013-10-12

In the title compound, C14H12ClN3O3S, the fused five- and six-membered rings are folded slightly along the common edge, forming a dihedral angle of 3.2 (1)°. The mean plane through the indazole system makes a dihedral angle of 30.75 (7)° with the distant benzene ring. In the crystal, N-H⋯O hydrogen bonds link the mol-ecules, forming a two-dimensional network parallel to (001).
Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429
Thermal dechlorination of PCB-209 over Ca species-doped Fe₂O₃.

PubMed

Su, Guijin; Huang, Linyan; Shi, Ruifang; Liu, Yexuan; Lu, Huijie; Zhao, Yuyang; Yang, Fan; Gao, Lirong; Zheng, Minghui

2016-02-01

Degradation reaction of decachlorobiphenyl (PCB-209) was investigated over the synthesized Ca species-doped Fe2O3 at 300 °C. The 1%Ca-Fe2O3 exhibited the highest activity among the four catalysts prepared with the pseudo-first order reaction at k(obs) = 0.103 min(-1). PCB-207, PCB-197, PCB-176, PCB-184, PCB-150, PCB-136, PCB-148, PCB-104, PCB-96, PCB-54, PCB-19, PCB-4 and PCB-1 were identified as the dominant isomers in their respective nonachlorobiphenyl (NonaCB) to monochlorobiphenyl (MonoCB) homologue groups. Analysis of the hydrodechlorination products indicated that dechlorination was much more favored on meta- and para-than on ortho-positions. The formation of significantly predominant NonaCB and octachlorobiphenyl (OctaCB) isomers was attributed to lower energy principles and to the 90° dihedral angles of two aromatic rings which prevented the hydrodechlorination at ortho-positions. When the number of chlorine atoms is not more than 7, the steric effect supports the formation of predominant PCB isomers having chlorines at four ortho-positions. During the dechlorination of tetrachlorobiphenyl (TetraCB) formed to generate monochlorobiphenyl (MonoCB) isomers, the chlorine atoms fully substituted at the ortho-positions have to be successively removed, with the first two dechlorinations preferentially occurring at the two different benzene rings. This is dissimilar to that of octachloronaphthalene (PCN-75) in which the hydrodechlorination reaction happened preferentially at ortho-position due to the existence of steric effects. The opposite roles of the steric effect in ortho-position between PCB-209 and PCN-75 might be due to the difference of the π-conjugated plane caused by the dihedral angle of 90° and 0° of the two aromatic rings. Copyright © 2015 Elsevier Ltd. All rights reserved.
Crystal structure of 2-((1E)-{2-[bis(2-methylbenzylsulfanyl)methylidene]hydrazin-1-ylidene}methyl)-6-methoxyphenol

PubMed Central

Yusof, Enis Nadia Md; Ravoof, Thahira Begum S. A.; Tahir, Mohamed Ibrahim Mohamed; Tiekink, Edward R. T.

2015-01-01

In the title compound, C25H26N2O2S2, the central CN2S2 atoms are almost coplanar (r.m.s. deviation = 0.0058 Å). One phenyl ring clearly lies to one side of the central plane, while the other is oriented in the plane but splayed. Despite the different relative orientations, the phenyl rings form similar dihedral angles of 64.90 (3) and 70.06 (3)° with the central plane, and 63.28 (4)° with each other. The benzene ring is twisted with respect to the central plane, forming a dihedral angle of 13.17 (7)°. The S2C=N, N—N and N—N=C bond lengths of 1.2919 (19), 1.4037 (17) and 1.2892 (19) Å, respectively, suggest limited conjugation over these atoms; the configuration about the N—N=C bond is E. An intramolecular O—H⋯N hydrogen bond is noted. In the crystal, phenyl–methoxy C—H⋯O and phenyl–phenyl C—H⋯π interactions lead to supramolecular double chains parallel to the b axis. These are connected into a layer via methyl–phenyl C—H⋯π interactions, and layers stack along the a axis, being connected by weak π–π interactions between phenyl rings [inter-centroid distance = 3.9915 (9) Å] so that a three-dimensional architecture ensues. PMID:26029435
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O 1 →4 -bonded polyglucose chains

NASA Astrophysics Data System (ADS)

Lubecka, Emilia A.; Liwo, Adam

2017-09-01

Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O ⋯O ⋯O virtual-bond angles (θ ) and for the dihedral angles for rotation about the O ⋯O virtual bonds (γ ) of 1 → 4 -linked glucosyl polysaccharides, for all possible combinations of [α ,β ]-[d,l]-glucose. The potentials of mean force corresponding to the virtual-bond angles and the virtual-bond dihedral angles were calculated from the free-energy surfaces of [α ,β ]-[d,l]-glucose pairs, determined by umbrella-sampling molecular-dynamics simulations with the AMBER12 force field, or combinations of the surfaces of two pairs sharing the overlapping residue, respectively, by integrating the respective Boltzmann factor over the dihedral angles λ for the rotation of the sugar units about the O ⋯O virtual bonds. Analytical expressions were subsequently fitted to the potentials of mean force. The virtual-bond-torsional potentials depend on both virtual-bond-dihedral angles and virtual-bond angles. The virtual-bond-angle potentials contain a single minimum at about θ =14 0° for all pairs except β -d-[α ,β ] -l-glucose, where the global minimum is shifted to θ =150° and a secondary minimum appears at θ =90°. The torsional potentials favor small negative γ angles for the α -d-glucose and extended negative angles γ for the β -d-glucose chains, as observed in the experimental structures of starch and cellulose, respectively. It was also demonstrated that the approximate expression derived based on Kubo's cluster-cumulant theory, whose coefficients depend on the identity of the disugar units comprising a trisugar unit that defines a torsional potential, fits simultaneously all torsional potentials very well, thus reducing the number of parameters significantly.
Normal- and oblique-shock flow parameters in equilibrium air including attached-shock solutions for surfaces at angles of attack, sweep, and dihedral

NASA Technical Reports Server (NTRS)

Hunt, J. L.; Souders, S. W.

1975-01-01

Normal- and oblique-shock flow parameters for air in thermochemical equilibrium are tabulated as a function of shock angle for altitudes ranging from 15.24 km to 91.44 km in increments of 7.62 km at selected hypersonic speeds. Post-shock parameters tabulated include flow-deflection angle, velocity, Mach number, compressibility factor, isentropic exponent, viscosity, Reynolds number, entropy difference, and static pressure, temperature, density, and enthalpy ratios across the shock. A procedure is presented for obtaining oblique-shock flow properties in equilibrium air on surfaces at various angles of attack, sweep, and dihedral by use of the two-dimensional tabulations. Plots of the flow parameters against flow-deflection angle are presented at altitudes of 30.48, 60.96, and 91.44 km for various stream velocities.
A simple molecular mechanics integrator in mixed rigid body and dihedral angle space

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

Vitalis, Andreas, E-mail: a.vitalis@bioc.uzh.ch; Pappu, Rohit V.

2014-07-21

We propose a numerical scheme to integrate equations of motion in a mixed space of rigid-body and dihedral angle coordinates. The focus of the presentation is biomolecular systems and the framework is applicable to polymers with tree-like topology. By approximating the effective mass matrix as diagonal and lumping all bias torques into the time dependencies of the diagonal elements, we take advantage of the formal decoupling of individual equations of motion. We impose energy conservation independently for every degree of freedom and this is used to derive a numerical integration scheme. The cost of all auxiliary operations is linear inmore » the number of atoms. By coupling the scheme to one of two popular thermostats, we extend the method to sample constant temperature ensembles. We demonstrate that the integrator of choice yields satisfactory stability and is free of mass-metric tensor artifacts, which is expected by construction of the algorithm. Two fundamentally different systems, viz., liquid water and an α-helical peptide in a continuum solvent are used to establish the applicability of our method to a wide range of problems. The resultant constant temperature ensembles are shown to be thermodynamically accurate. The latter relies on detailed, quantitative comparisons to data from reference sampling schemes operating on exactly the same sets of degrees of freedom.« less
4-[(1-Benzyl-1H-1,2,3-triazol-4-yl)methoxy]benzene-1,2-dicarbonitrile: crystal structure, Hirshfeld surface analysis and energy-minimization calculations

PubMed Central

Shamsudin, Norzianah; Tan, Ai Ling; Young, David J.; Jotani, Mukesh M.; Otero-de-la-Roza, A.; Tiekink, Edward R. T.

2016-01-01

In the solid state, the title compound, C18H13N5O, adopts a conformation whereby the phenyl ring and methoxy–benzene-1,2-dicarbonitrile residue (r.m.s. deviation of the 12 non-H atoms = 0.041 Å) lie to opposite sides of the central triazolyl ring, forming dihedral angles of 79.30 (13) and 64.59 (10)°, respectively; the dihedral angle between the outer rings is 14.88 (9)°. This conformation is nearly 7 kcal mol−1 higher in energy than the energy-minimized structure which has a syn disposition of the outer rings, enabling intramolecular π–π interactions. In the crystal, methylene-C—H⋯N(triazolyl) and carbonitrile-N⋯π(benzene) interactions lead to supramolecular chains along the a axis. Supramolecular layers in the ab plane arise as the chains are connected by benzene-C—H⋯N(carbonitrile) interactions; layers stack with no directional interactions between them. The specified intermolecular contacts along with other, weaker contributions to the supramolecular stabilization are analysed in a Hirshfeld surface analysis. PMID:27375890
1-(4,4''-Difluoro-5'-meth-oxy-1,1':3',1''-terphenyl-4'-yl)ethanone.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Samshuddin, S; Narayana, B; Sarojini, B K

2012-01-01

In the title compound, C(21)H(16)F(2)O(2), the central benzene ring is inclined at dihedral angles of 30.91 (8) and 46.88 (7)° to the two terminal fluoro-substituted rings. The dihedral angle between the two terminal fluoro-subsituted rings is 68.34 (8)°. An intra-molecular C-H⋯O hydrogen bond generates an S(6) ring motif. The crystal structure is stabilized by weak C-H⋯π inter-actions.
N-(3-Chloro-1H-indazol-5-yl)-4-methoxybenzenesulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

In the title compound, C14H12ClN3O3S, the fused five- and six-membered rings are folded slightly along the common edge, forming a dihedral angle of 3.2 (1)°. The mean plane through the indazole system makes a dihedral angle of 30.75 (7)° with the distant benzene ring. In the crystal, N—H⋯O hydrogen bonds link the molecules, forming a two-dimensional network parallel to (001). PMID:24454078

Imidazolium 3-nitrobenzoate

PubMed Central

Hou, Guang-Yang; Zhou, Li-Na; Yin, Qiu-Xiang; Su, Wei-Yi; Mao, Hui-Lin

2009-01-01

In the title compound, C3H5N2 +·C7H4NO4 −, the benzene ring forms a dihedral angle of 40.60 (5)° with the imidizolium ring. The nitrobenzoate anion is approximately planar: the benzene ring makes dihedral angles of 3.8 (3) and 3.2 (1)° with the nitro and carboxylate groups, respectively. In the crystal structure, the cations and anions are linked by intermolecular N—H⋯O hydrogen bonds, forming a zigzag chain along the b axis. PMID:21583857
Methyl 4-amino-3-methylbenzoate

PubMed Central

Li, Xiang; Yuan, Lian-Shan; Wang, Dan; Liu, Shan; Yao, Cheng

2008-01-01

In the molecule of the title compound, C9H11NO2, the methyl C and amino N atoms bonded to the benzene ring lie in the ring plane. Intramolecular C—H⋯O hydrogen bonding results in the formation of a five-membered planar ring, which is oriented at a dihedral angle of 2.73 (3)° with respect to the benzene ring, so they are nearly coplanar. In the crystal structure, intermolecular N—H⋯O hydrogen bonds link the molecules into chains elongated along the c axis and stacked along the b axis. PMID:21202370
Biased Metropolis Sampling for Rugged Free Energy Landscapes

NASA Astrophysics Data System (ADS)

Berg, Bernd A.

2003-11-01

Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which uses probability densities from a higher temperature to improve the algorithmic performance at a lower temperature. The method is suitable for canonical as well as for generalized ensemble simulations. A simple approximation to the full transformation is tested at room temperature for Met-Enkephalin in vacuum. Integrated autocorrelation times are found to be reduced by factors close to two and a similar improvement due to generalized ensemble methods enters multiplicatively.
1-(2-Cyanoethyl)-2-(2-pyridyl)-1H,3H-benzimidazol-3-ium perchlorate

PubMed Central

Li, Yan; Tang, Xiaoliang; Chen, Jiayu; Wu, Daxiang; Liu, Weisheng

2010-01-01

The title compound, C15H13N4 +·ClO4 −, comprises a nonplanar 1-(2-cyanoethyl)-2-(2-pyridyl)-1H,3H-benzimidazol-3-ium cation [dihedral angle between the imidazole and pyridine rings = 22.5 (8)°] and a perchlorate anion. The cation is formed by protonation of the N atom of the benzimidazole ring. A charged N—H⋯O hydrogen bond connects the anion and cation, and intermolecular C—H⋯O and C—H⋯N interactions contribute to the crystal packing. PMID:21579831
Crystal structure of N-(3-chloro-1-methyl-1H-indazol-5-yl)-4-methoxybenzenesulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Gamouh, Ahmed; Saadi, Mohamed; El Ammari, Lahcen

2014-01-01

In the title compound, C15H14ClN3O3S, the dihedral angle between the planes of the indazole ring system (r.m.s. deviation = 0.007 Å) and the benzene ring is 89.05 (7)°. The methoxy C atom deviates from its attached ring by 0.196 (3) Å. In the crystal, inversion dimers linked by pairs of N—H⋯O hydrogen bonds generate R 2 2(8) loops. The dimers are connected into [010] chains by C—H⋯O interactions. PMID:25309293
Discrete Haar transform and protein structure.

PubMed

Morosetti, S

1997-12-01

The discrete Haar transform of the sequence of the backbone dihedral angles (phi and psi) was performed over a set of X-ray protein structures of high resolution from the Brookhaven Protein Data Bank. Afterwards, the new dihedral angles were calculated by the inverse transform, using a growing number of Haar functions, from the lower to the higher degree. New structures were obtained using these dihedral angles, with standard values for bond lengths and angles, and with omega = 0 degree. The reconstructed structures were compared with the experimental ones, and analyzed by visual inspection and statistical analysis. When half of the Haar coefficients were used, all the reconstructed structures were not yet collapsed to a tertiary folding, but they showed yet realized most of the secondary motifs. These results indicate a substantial separation of structural information in the space of Haar transform, with the secondary structural information mainly present in the Haar coefficients of lower degrees, and the tertiary one present in the higher degree coefficients. Because of this separation, the representation of the folded structures in the space of Haar transform seems a promising candidate to encompass the problem of premature convergence in genetic algorithms.
A 2:1 co-crystal of 2-methyl-benzoic acid and N,N'-bis-(pyridin-4-ylmeth-yl)ethanedi-amide: crystal structure and Hirshfeld surface analysis.

PubMed

Syed, Sabrina; Jotani, Mukesh M; Halim, Siti Nadiah Abdul; Tiekink, Edward R T

2016-03-01

The asymmetric unit of the title 2:1 co-crystal, 2C8H8O2·C14H14N4O2, comprises an acid mol-ecule in a general position and half a di-amide mol-ecule, the latter being located about a centre of inversion. In the acid, the carb-oxy-lic acid group is twisted out of the plane of the benzene ring to which it is attached [dihedral angle = 28.51 (8)°] and the carbonyl O atom and methyl group lie approximately to the same side of the mol-ecule [hy-droxy-O-C-C-C(H) torsion angle = -27.92 (17)°]. In the di-amide, the central C4N2O2 core is almost planar (r.m.s. deviation = 0.031 Å), and the pyridyl rings are perpendicular, lying to either side of the central plane [central residue/pyridyl dihedral angle = 88.60 (5)°]. In the mol-ecular packing, three-mol-ecule aggregates are formed via hy-droxy-O-H⋯N(pyrid-yl) hydrogen bonds. These are connected into a supra-molecular layer parallel to (12[Formula: see text]) via amide-N-H⋯O(carbon-yl) hydrogen bonds, as well as methyl-ene-C-H⋯O(amide) inter-actions. Significant π-π inter-actions occur between benzene/benzene, pyrid-yl/benzene and pyrid-yl/pyridyl rings within and between layers to consolidate the three-dimensional packing.
Electromagnetic backscattering by corner reflectors

NASA Technical Reports Server (NTRS)

Balanis, C. A.; Griesser, T.

1986-01-01

The Geometrical Theory of Diffraction (GTD), which supplements Geometric Optics (GO), and the Physical Theory of Diffraction (PTD), which supplements Physical Optics (PO), are used to predict the backscatter cross sections of dihedral corner reflectors which have right, obtuse, or acute included angles. These theories allow individual backscattering mechanisms of the dihedral corner reflectors to be identified and provide good agreement with experimental results in the azimuthal plane. The advantages and disadvantages of the geometrical and physical theories are discussed in terms of their accuracy, usefulness, and complexity. Numerous comparisons of analytical results with experimental data are presented. While physical optics alone is more accurate and more useful than geometrical optics alone, the combination of geometrical optics and geometrical diffraction seems to out perform physical optics and physical diffraction when compared with experimental data, especially for acute angle dihedral corner reflectors.
Piperidinium bis(2-oxidobenzoato-κ2 O 1,O 2)borate

PubMed Central

Tang, Zhi-Hua; Huang, Chaojun

2009-01-01

The asymmetric unit of the title compound, C5H12N+·C14H8BO6 − or [C5H12N][BO4(C7H4O)2], contains two piperidinium cations and two bis(salicylato)borate anions. The coordination geometries around the B atoms are distorted tetrahedral. In the two molecules, the aromatic rings are oriented at dihedral angles of 76.27 (3) and 83.86 (3)°. The rings containing B atoms have twist-boat conformations, while the two cations adopt chair conformations. In the crystal, the component species are linked by N—H⋯O hydrogen bonds. In the crystal structure, intra- and intermolecular N—H⋯O hydrogen bonds link the molecules. PMID:21581628
4-[(E)-(2,4-Difluorophenyl)(hydroxyimino)methyl]piperidinium picrate

PubMed Central

Jasinski, Jerry P.; Butcher, Ray J.; Yathirajan, H. S.; Mallesha, L.; Mohana, K. N.

2009-01-01

The title compound, C12H15F2N2O+·C6H2N3O7 −, a picrate salt of 4-[(E)-(2,4-difluorophenyl)(hydroxyimino)methyl]piperidine, crystallizes with two independent molecules in a cation–anion pair in the asymmetric unit. In the cation, a methyl group is trisubstituted by hydroxyimino, piperidin-4-yl and 2,4-difluorophenyl groups, the latter of which contains an F atom disordered over two positions in the ring [occupancy ratio 0.631 (4):0.369 (4)]. The mean plane of the hydroxy group is in a synclinical conformation nearly orthogonal [N—C—C—C = 72.44 (19)°] to the mean plane of the piperidine ring, which adopts a slightly distorted chair conformation. The dihedral angle between the mean plane of the 2,4-difluorophenyl and piperidin-4-yl groups is 60.2 (3)°. In the picrate anion, the mean planes of the two o-NO2 and single p-NO2 groups adopt twist angles of 5.7 (2), 25.3 (7) and 8.3 (6)°, respectively, with the attached planar benzene ring. The dihedral angle between the mean planes of the benzene ring in the picrate anion and those in the hydroxyimino, piperidin-4-yl and 2,4-difluorophenyl groups in the cation are 84.9 (7), 78.9 (4) and 65.1 (1)°, respectively. Extensive hydrogen-bond interactions occur between the cation–anion pair, which help to establish the crystal packing in the unit cell. This includes dual three-center hydrogen bonds with the piperidin-4-yl group, the phenolate and o-NO2 O atoms of the picrate anion at different positions in the unit cell, which form separate N—H⋯(O,O) bifurcated intermolecular hydrogen-bond interactions. Also, the hydroxy group forms a separate hydrogen bond with a nearby piperidin-4-yl N atom, thus providing two groups of hydrogen bonds, which form an infinite two-dimensional network along (011). PMID:21577832
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.
Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775
Crystal structure of di-μ-chlorido-bis-(chlorido-{N1,N1-diethyl-N4-[(pyridin-2-yl-κN)methyl-idene]benzene-1,4-di-amine-κN4}mercury(II)).

PubMed

Faizi, Md Serajul Haque; Dege, Necmi; Goleva, Kateryna

2017-06-01

The title dinuclear mercury(II) complex, [Hg 2 Cl 4 (C 16 H 19 N 3 ) 2 ], synthesized from the pyridine-derived Schiff base ( E )- N 1 , N 1 -diethyl- N 4 -[(pyridin-2-yl)methyl-idene]benzene-1,4-di-amine (DPMBD), has inversion symmetry. The five-coordinated Hg II atoms have distorted square-pyramidal stereochemistry comprising two N-atom donors from bidentate chelate BPMBD ligands and three Cl-atom donors, two bridging and one monodentate. The dihedral angle between the benzene and the pyridine rings in the BPMBD ligand is 7.55 (4)°. In the crystal, the dinuclear mol-ecules are linked by weak C-H⋯Cl hydrogen bonds, forming zigzag ribbons lying parallel to [001]. Also present in the structure are π-π inter-actions between benzene and pyridine rings [minimum ring-centroid separation = 3.698 (8) Å].
Crystal structure of rubidium methyl-diazo-tate.

PubMed

Grassl, Tobias; Korber, Nikolaus

2017-02-01

The title compound, Rb + ·H 3 CN 2 O - , has been crystallized in liquid ammonia as a reaction product of the reductive ammonolysis of the natural compound streptozocin. Elemental rubidium was used as reduction agent as it is soluble in liquid ammonia, forming a blue solution. Reductive bond cleavage in biogenic materials under kinetically controlled conditions offers a new approach to gain access to sustainably produced raw materials. The anion is nearly planar [dihedral angle O-N-N-C = -0.4 (2)°]. The Rb + cation has a coordination number of seven, and coordinates to five anions. One anion is bound via both its N atoms, one by both O and N, two anions are bound by only their O atoms, and the last is bound via the N atom adjacent to the methyl group. The diazo-tate anions are bridged by cations and do not exhibit any direct contacts with each other. The cations form corrugated layers that propagate in the (-101) plane.
A fast and accurate dihedral interpolation loop subdivision scheme

NASA Astrophysics Data System (ADS)

Shi, Zhuo; An, Yalei; Wang, Zhongshuai; Yu, Ke; Zhong, Si; Lan, Rushi; Luo, Xiaonan

2018-04-01

In this paper, we propose a fast and accurate dihedral interpolation Loop subdivision scheme for subdivision surfaces based on triangular meshes. In order to solve the problem of surface shrinkage, we keep the limit condition unchanged, which is important. Extraordinary vertices are handled using modified Butterfly rules. Subdivision schemes are computationally costly as the number of faces grows exponentially at higher levels of subdivision. To address this problem, our approach is to use local surface information to adaptively refine the model. This is achieved simply by changing the threshold value of the dihedral angle parameter, i.e., the angle between the normals of a triangular face and its adjacent faces. We then demonstrate the effectiveness of the proposed method for various 3D graphic triangular meshes, and extensive experimental results show that it can match or exceed the expected results at lower computational cost.
7-Chloro-5-(2-ethoxyphenyl)-1-methyl-3-propyl-2,6-dihydro-1H-pyrazolo[4,3-d]pyrimidine

PubMed Central

Zhou, Ming-Qiu; Zhu, Kai; Lv, Xiao-Ping; Han, Ping-Fang; Wei, Ping

2009-01-01

In the title compound, C17H21ClN4O, the benzene ring is oriented at dihedral angles of 1.59 (3) and 1.27 (3)° with respect to the pyrimidine and pyrazole rings, while the dihedral angle between the pyrimidine and pyrazole rings is 0.83 (3)°. An intramolecular N—H⋯O hydrogen bond results in the formation of a planar (r.m.s. deviation 0.004 Å) six-membered ring. PMID:21577789
4-(4-Methoxyphenyl)-1-phenylpyridine-2,6(1H,3H)-dione

PubMed Central

Das, Ushati; Chheda, Shardul B.; Pednekar, Suhas R.; Karambelkar, Narendra P.; Guru Row, T. N.

2009-01-01

In the title compound, C18H15NO3, the pyridine-2,6-dione ring adopts an envelope conformation. The phenyl ring lies approximately perpendicular to the mean plane of the pyridine-2,6-dione ring [dihedral angle = 81.5 (1)°], while the methoxyphenyl ring is tilted to the same plane by a dihedral angle of 34.8 (1)°. Intermolecular C—H⋯O interactions link the molecules into chains along [100]. PMID:21583176
3-[Bis(dimethylamino)methylene]-1,1-diphenylurea

PubMed Central

Tiritiris, Ioannis

2012-01-01

In the title compound, C18H22N4O, the C=N and C—N bond lengths in the CN3 unit are 1.3179 (11), 1.3551 (11) and 1.3737 (11) Å, indicating double- and single-bond character, respectively. The N—C—N angles are 115.91 (8), 118.20 (8) and 125.69 (8), showing a deviation of the CN3 plane from an ideal trigonal–planar geometry. The bonds between the N atoms and the terminal C-methyl groups all have values close to a typical single bond [1.4529 (12)–1.4624 (12) Å]. The dihedral angle between the phenyl rings is 79.63 (4)°. In the crystal, the molecules are connected via weak C—H⋯O hydrogen bonds, generating chains along [100]. PMID:23284417
Synthesis and crystal structure of the iridium(I) carbene complex with a pair of hydrogen wing tips

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

Huang, H.-Y.; Chen, Z.-M.; Wang, Y.

The iridium(I) cyclooctadiene complex with two (3-tert-butylimidazol-2-ylidene) ligands [(H-Im{sup t}Bu){sub 2}Ir(COD)]{sup +}PF{sub 6}{sup −} (C{sub 22}H{sub 32}PF{sub 6}IrN{sub 4}) has been prepared, and its crystal structure is determined by X-ray diffraction. Complex exhibits slightly distorted square planar configurations around the metal atom, which is coordinated by two H-Im{sup t}Bu ligands and one cyclooctadiene group. The new iridium carbene complex has a pair of hydrogen wing tips. The Ir−C{sub carbene} bond lengths are 2.066(5) and 2.052(5) Å, and the bond angle C−Ir−C between these bonds is 95.54(19)°. The dihedral angle between two imidazol-2-ylidene rings is 86.42°.
Diethyl 2,2'-(ethane-1,2-diyldi-oxy)di-benzo-ate.

PubMed

Shi, Huaduan; Qin, Haisha; Ma, Zhen

2014-05-01

The mol-ecular title compound, C20H22O6, was obtained by the reaction of ethyl 2-hy-droxy-benzoate with 1,2-di-chloro-ethane. The mol-ecule lies on a twofold rotation axis which passes through the middle of the central ethyl-ene bridge. This group exhibits a gauche conformation with the corresponding O-C-C-O torsion angle being 73.2 (2)°. The C atoms of the carboxyl group, the aryl and the O-CH2 group are coplanar, with an r.m.s. deviation of 0.01 Å. The two aryl rings form a dihedral angle of 67.94 (4)°. The ester ethyl group is disordered over two sets of sites with an occupancy ratio of 0.59 (2):0.41 (2). The crystal packing is dominated by van der Waals forces.

New force field for molecular simulation of guanidinium-based ionic liquids.

PubMed

Liu, Xiaomin; Zhang, Suojiang; Zhou, Guohui; Wu, Guangwen; Yuan, Xiaoliang; Yao, Xiaoqian

2006-06-22

An all-atom force field was proposed for a new class of room temperature ionic liquids (RTILs), N,N,N',N'-tetramethylguanidinium (TMG) RTILs. The model is based on the AMBER force field with modifications on several parameters. The refinements include (1) fitting the vibration frequencies for obtaining force coefficients of bonds and angles against the data obtained by ab initio calculations and/or by experiments and (2) fitting the torsion energy profiles of dihedral angles for obtaining torsion parameters against the data obtained by ab initio calculations. To validate the force field, molecular dynamics (MD) simulations at different temperatures were performed for five kinds of RTILs, where TMG acts as a cation and formate, lactate, perchlorate, trifluoroacetate, and trifluoromethylsulfonate act as anions. The predicted densities were in good agreement with the experimental data. Radial distribution functions (RDFs) and spatial distribution functions (SDFs) were investigated to depict the microscopic structures of the RTILs.
Crystal structure of N-(1-allyl-3-chloro-1H-indazol-5-yl)-4-methyl-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Chigr, Mohamed; Saadi, Mohamed; El Ammari, Lahcen

2014-09-01

The 3-chloro-1H-indazole system in the title mol-ecule, C17H16ClN3O2S, is almost planar, with the largest deviation from the mean plane being 0.029 (2) Å for one of the N atoms. This system is nearly perpendicular to the allyl chain, as indicated by the C-C-N-N torsion angle of -90.1 (6)° between them. The allyl group is split into two fragments, the major component has a site occupancy of 0.579 (7). The indazole system makes a dihedral angle of 47.53 (10)° with the plane through the benzene ring. In the crystal, mol-ecules are connected by N-H⋯O and C-H⋯O hydrogen bonds, forming a three-dimensional network.
Crystal structure of N-(1-allyl-3-chloro-1H-indazol-5-yl)-4-methylbenzenesulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Chigr, Mohamed; Saadi, Mohamed; El Ammari, Lahcen

2014-01-01

The 3-chloro-1H-indazole system in the title molecule, C17H16ClN3O2S, is almost planar, with the largest deviation from the mean plane being 0.029 (2) Å for one of the N atoms. This system is nearly perpendicular to the allyl chain, as indicated by the C—C—N—N torsion angle of −90.1 (6)° between them. The allyl group is split into two fragments, the major component has a site occupancy of 0.579 (7). The indazole system makes a dihedral angle of 47.53 (10)° with the plane through the benzene ring. In the crystal, molecules are connected by N—H⋯O and C—H⋯O hydrogen bonds, forming a three-dimensional network. PMID:25309215
Bromido({2-[2-(diphenylphosphanyl)benzylidene]hydrazin-1-ylidene}(4-methoxyanilino)methanethiolato)palladium(II) acetone monosolvate

PubMed Central

Mokthar, Khalisah Asilah; Shamsuddin, Mustaffa; Rosli, Mohd Mustaqim; Fun, Hoong-Kun

2012-01-01

In the title compound, [PdBr(C27H23N3OPS)]·C3H6O, the coordination geometry about the PdII atom is distorted square-planar, arising from the attached Br, S, P and N atoms (N and Br are trans), the maximum deviation from the plane being 0.2053 (4) Å for the N atom. The three benzene rings attached to the P atom make dihedral angles of 69.78 (7), 87.05 (7) and 77.50 (7)° with each other. An intramolecular C—H⋯N hydrogen bond forms an S(6) ring motif. In the crystal, the complex molecules form infinite chains along the a-axis direction through C—H⋯Br interactions, and a C—H⋯O interaction links the main molecule with the acetone solvent molecule. PMID:22807805
Aqua{6,6′-dimethoxy-2,2′-[ethane-1,2-diylbis(nitrilomethylidyne)]diphenolato}nickel(II)

PubMed Central

Guo, Zhenghua; Li, Lianzhi; Xu, Tao; Li, Jinghong; Wang, Daqi

2009-01-01

The title complex, [Ni(C18H18N2O4)(H2O)], lies on a mirror plane with the NiII ion coordinated by two N and two O atoms of a tetradentate Schiff base ligand and one water O atom in a distorted square-pyramidal enviroment. The –CH2–CH2– group of the ligand is disordered equally over two sites about the mirror plane. The dihedral angle between the mean planes of the two symmetry-related chelate rings is 37.16 (6)°. In the crystal structure, intermolecular O—H⋯O hydrogen bonds link complex molecules into one-dimensional chains along [100] and these chains are linked, in turn, by very weak intermolecular C—H⋯O hydrogen bonds into a two-dimensional network. PMID:21577698
Rotational study on the van der Waals complex 1-chloro-1,1-difluoroethane-argon.

PubMed

Wang, Juan; Chen, Junhua; Feng, Gang; Xia, Zhining; Gou, Qian

2018-03-15

The rotational spectrum of the van der Waals complex formed between 1-chloro-1,1-difluoroethane and argon has been investigated by using a pulsed jet Fourier transform microwave spectrometer. Only one set of rotational transitions belonging to the lowest energy conformer has been observed and assigned, although theoretical calculations suggest six stable conformers that might be observed. The observed conformer, according to the experimental evidence from two isotopologues ( 35 Cl and 37 Cl), adopts a configuration in which the argon atom is located, close to the CF 2 Cl top, between the CCF and CCCl planes (the dihedral angle ∠ArCCCl is 65.2°). The distance between argon atom and the center of mass of CH 3 CF 2 Cl is 3.949(2) Å. The dissociation energy, with pseudo diatomic approximation, is evaluated to be 2.4kJmol -1 . Copyright © 2017 Elsevier B.V. All rights reserved.
Rotational study on the van der Waals complex 1-chloro-1,1-difluoroethane-argon

NASA Astrophysics Data System (ADS)

Wang, Juan; Chen, Junhua; Feng, Gang; Xia, Zhining; Gou, Qian

2018-03-01

The rotational spectrum of the van der Waals complex formed between 1-chloro-1,1-difluoroethane and argon has been investigated by using a pulsed jet Fourier transform microwave spectrometer. Only one set of rotational transitions belonging to the lowest energy conformer has been observed and assigned, although theoretical calculations suggest six stable conformers that might be observed. The observed conformer, according to the experimental evidence from two isotopologues (35Cl and 37Cl), adopts a configuration in which the argon atom is located, close to the sbnd CF2Cl top, between the CCF and CCCl planes (the dihedral angle ∠ ArCCCl is 65.2°). The distance between argon atom and the center of mass of CH3CF2Cl is 3.949(2) Å. The dissociation energy, with pseudo diatomic approximation, is evaluated to be 2.4 kJ mol- 1.
(2-{[2-(1H-Benzimidazol-2-yl-κN 3)phenyl]iminomethyl-κN}-5-methylphenolato-κO)chloridozinc(II)

PubMed Central

Eltayeb, Naser Eltaher; Teoh, Siang Guan; Chantrapromma, Suchada; Fun, Hoong-Kun

2011-01-01

In the title mononuclear complex, [Zn(C21H16N3O)Cl], the ZnII ion is coordinated in a distorted tetrahedral geometry by two benzimidazole N atoms and one phenolate O atom from the tridentate Schiff base ligand and a chloride ligand. The benzimidazole ring system forms dihedral angles of 26.68 (9) and 56.16 (9)° with the adjacent benzene ring and the methylphenolate group benzene ring, respectively. In the crystal, molecules are linked by N—H⋯Cl hydrogen bonds into chains along [100]. Furthermore, weak C—H⋯O and C—H⋯π interactions, in addition to π–π interactions with centroid–centroid distances in the range 3.5826 (13)–3.9681 (13) Å, are also observed. PMID:22065469
Methyl 4-(4-fluorophenyl)-6-isopropyl-2-[N-methyl-N-(methylsulfonyl)amino]pyrimidine-5-carboxylate

PubMed Central

He, Wei; Yang, Dong-Ling; Cui, Yong-Tao; Xu, Ye-Ming; Guo, Cheng

2008-01-01

In the molecule of the title compound, C17H20FN3O4S, the pyrimidine and benzene rings are oriented at a dihedral angle of 35.59 (3)°. Intramolecular C—H⋯N and C—H⋯O hydrogen bonds result in the formation of one five- and two six-membered non-planar rings. One of the six-membered rings adopts a chair conformation, while the other six-membered ring and the five-membered ring exhibit envelope conformations with O and N atoms displaced by 0.837 (3) and 0.152 (3) Å, respectively from the planes of the other ring atoms. In the crystal structure, intermolecular C—H⋯F hydrogen bonds link the molecules into infinite chains. PMID:21202637
How main-chains of proteins explore the free-energy landscape in native states.

PubMed

Senet, Patrick; Maisuradze, Gia G; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A

2008-12-16

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein (crambin) and a beta-sheet polypeptide (BS2) in their "native" states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C(alpha) atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.
How main-chains of proteins explore the free-energy landscape in native states

PubMed Central

Senet, Patrick; Maisuradze, Gia G.; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A.

2008-01-01

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an α/β protein (crambin) and a β-sheet polypeptide (BS2) in their “native” states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive Cα atoms, increases as a power law of time, tα, with an exponent α between 0.08 and 0.39 (α = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles. PMID:19073932
Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

NASA Astrophysics Data System (ADS)

Sicard, François; Senet, Patrick

2013-06-01

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.
Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics.

PubMed

Sicard, François; Senet, Patrick

2013-06-21

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.
Effect of Tail Dihedral on Lateral Control Effectiveness at High Subsonic Speeds of Differentially Deflected Horizontal-Tail Surfaces on a Configuration having a Thin Highly Tapered Wing

NASA Technical Reports Server (NTRS)

Fournier, Paul G.

1959-01-01

Tests have been conducted in the Langley high-speed 7- by 10-foot tunnel to determine the effect of tail dihedral on lateral control effectiveness of a complete-model configuration having differentially deflected horizontal-tail surfaces. Limited tests were made to determine the lateral characteristics as well as the longitudinal characteristics in sideslip. The wing had an aspect ratio of 3, a taper ratio of 0.14, 28.80 deg sweep of the quarter-chord line with zero sweep at the 80-percent-chord line, and NACA 65A004 airfoil sections. The test Mach number range extended from 0.60 to 0.92. There are only small variations in the roll effectiveness parameter C(sub iota delta) with negative tail dihedral angle. The tail size used on the test model, however, is perhaps inadequate for providing the roll rates specified by current military requirements at subsonic speeds. The lateral aerodynamic characteristics were essentially constant throughout the range of sideslip angle from 12 deg to -12 deg. A general increase in yawing moment was noted with increased negative dihedral throughout the Mach number range.
Crystal structure of 2-benzoylamino-N′-(4-hydroxybenzylidene)-3-(thiophen-2-yl)prop-2-enohydrazide

PubMed Central

Subbulakshmi, Karanth N.; Narayana, Badiadka; Yathirajan, Hemmige S.; Jasinski, Jerry P.; Rathore, Ravindranath S.; Glidewell, Christopher

2016-01-01

In the title compound, C21H17N3O3S, the non-H atoms, apart from those in the benzoyl group, are almost coplanar (r.m.s. deviation = 0.049 Å) and the benzoyl group is almost orthogonal to the plane of the rest of the molecule [dihedral angle = 80.34 (6)°]. In the crystal, a combination of N—H⋯O and asymmetric bifurcated O—H⋯(N,O) hydrogen bonds link the molecules into a three-dimensional network. Weak C—H⋯O interactions are also observed. PMID:27536390
7-Chloro-5-cyclopropyl-9-methyl-5H-4,5,6,10-tetraazadibenzo[a,d]cyclohepten-11(10H)-one

PubMed Central

Naveen, S.; Thimmegowda, N. R.; Manjunath, H. R.; Sridhar, M. A.; Prasad, J. Shashidhara; Rangappa, K. S.

2011-01-01

In the title compound, C15H13ClN4O, which is a chloro derivative of the drug Nevirapine, the diazepine ring is in a twisted boat conformation. The pyridine rings fused to the diazepine fragment form a dihedral angle of 58.44 (10)° and the molecule adopts a butterfly shape. The molecules are joined via N—H⋯N hydrogen bonding into polymeric chains down the b axis. All weaker C—H⋯O interactions involve the carbonyl O atom as acceptor. PMID:21754822
2-[4-(2-Chloro-acet-yl)phen-yl]-2-methyl-1-(pyrrolidin-1-yl)propan-1-one.

PubMed

Ren, Dong-Mei

2013-01-01

The asymmetric unit of the title compound, C16H20ClNO2, contains two mol-ecules in which the dihedral angles between the benzene ring and the plane of the amide unit are 77.4 (1) and 81.1 (1)°. In both mol-ecules, the five-membered ring adopts an envelope conformation with one of the β-C atoms as the flap. In the crystal, mol-ecules are connected via C-H⋯O hydrogen bonds, forming chains along the b-axis direction. These chains are further linked by C-H⋯π inter-actions, forming a three-dimensional network.
A Geometric Principle May Guide Self-Assembly of Fullerene Cages from Clathrin Triskelia and from Carbon Atoms☆

PubMed Central

Schein, Stan; Sands-Kidner, Michelle

2008-01-01

Abstract Clathrin triskelia and carbon atoms alike self-assemble into a limited selection of fullerene cages (with n three connected vertices, 3n/2 edges, 12 pentagonal faces, and (n−20)/2 hexagonal faces). We show that a geometric constraint—exclusion of head-to-tail dihedral angle discrepancies (DADs)—explains this limited selection as well as successful assembly into such closed cages in the first place. An edge running from a pentagon to a hexagon has a DAD, since the dihedral angles about the edge broaden from its pentagon (tail) end to its hexagon (head) end. Of the 21 configurations of a central face and surrounding faces, six have such DAD vectors arranged head-to-tail. Of the 5770 mathematically possible fullerene cages for n ≤ 60, excluding those with any of the six configurations leaves just 15 cages plus buckminsterfullerene (n = 60), among them the known clathrin cages. Of the 216,739 mathematically possible cages for 60 < n ≤ 84, just the 50 that obey the isolated-pentagon rule, among them known carbon cages, pass. The absence of likely fullerenes for some n (30,34,46,48,52–58,62–68) explains the abundance of certain cages, including buckminsterfullerene. These principles also suggest a “probable roads” path to self-assembly in place of pentagon-road and fullerene-road hypotheses. PMID:17921209
Teaching Molecular Symmetry of Dihedral Point Groups by Drawing Useful 2D Projections

ERIC Educational Resources Information Center

Chen, Lan; Sun, Hongwei; Lai, Chengming

2015-01-01

There are two main difficulties in studying molecular symmetry of dihedral point groups. One is locating the C[subscript 2] axes perpendicular to the C[subscript n] axis, while the other is finding the s[subscript]d planes which pass through the C[subscript n] axis and bisect the angles formed by adjacent C[subscript 2] axes. In this paper, a…
N-(3-Chloro-1-methyl-1H-indazol-5-yl)-4-methylbenzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Amiri, Ouafa; Saadi, Mohamed; El Ammari, Lahcen

2014-02-01

The asymmetric unit of the title compound, C15H14ClN3O2S, contains two independent mol-ecules showing different conformations: in one mol-ecule, the indazole ring system makes a dihedral angle of 51.5 (1)° with the benzene ring whereas in the other, the indazole unit is almost perpendicular to the benzene ring [dihedral angle 77.7 (1)°]. In the crystal, the mol-ecules are linked by N-H⋯N and N-H⋯O hydrogen bonds, forming a set of four mol-ecules linked in pairs about an inversion centre.

2,3-Diphenylquinoxalin-1-ium chloride

PubMed Central

Wu, Wen-Sheng

2010-01-01

The title compound, C20H15N2 +·Cl−, was prepared by the reaction of benzil with o-phenylenediamine in refluxing ethanol and then crystallized in 5% hydrochloric acid. The two phenyl rings are oriented at dihedral angles of 50.93 (8) and 50.28 (8)° with respect to the quinoxalin-1-ium ring system. The dihedral angle between the two phenyl rings is 56.71 (10)°. In the crystal, the cations and anions are linked by N—H⋯Cl and C—H⋯Cl interactions, forming chains along the b axis. PMID:21588016
Molecular Dynamics Simulation of γS-WT and γS-G18V

NASA Astrophysics Data System (ADS)

Ozawa, Ai; Yamada, Hironao; Mori, Sakiko; Noguchi, Yoh; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako

γS-crystallin maintains transparency of the crystalline lens and increases the refraction index of lens. γS-G18V is a mutant γS-crystallin in which 18th glycine is replaced by valine. This protein is related to childhood-onset cortical cataract. In this paper, we study the fluctuation of residues and dihedral angles, and investigate the difference between γS-WT and γS-G18V by using molecular dynamics simulation. In the result of RMSF, we found large difference around the mutation point. In addition, differences of dihedral angles of cysteins were found in this area.
Crystal and mol-ecular structure of (2Z,5Z)-3-(2-meth-oxy-phen-yl)-2-[(2-meth-oxy-phen-yl)imino]-5-(4-nitro-benzyl-idene)thia-zolidin-4-one.

PubMed

Djafri, Ahmed; Chouaih, Abdelkader; Daran, Jean-Claude; Djafri, Ayada; Hamzaoui, Fodil

2017-04-01

In the title compound, C 24 H 19 N 3 O 5 S, the thia-zole ring (r.m.s. deviation = 0.012 Å) displays a planar geometry and is surrounded by three fragments, two meth-oxy-phenyl and one nitro-phenyl. The thia-zole ring is almost in the same plane as the nitro-phenyl ring, making a dihedral angle of 20.92 (6)°. The two meth-oxy-phenyl groups are perpendicular to the thia-zole ring [dihedral angles of 79.29 (6) and 71.31 (7)° and make a dihedral angle of 68.59 (7)°. The mol-ecule exists in an Z , Z conformation with respect to the C=N imine bond. In the crystal, a series of C-H⋯N, C-H⋯O and C-H⋯S hydrogen bonds, augmented by several π-π(ring) inter-actions, produce a three-dimensional architecture of mol-ecules stacked along the b -axis direction. The experimentally derived structure is compered with that calculated theoretically using DFT(B3YLP) methods.
Structural modeling of djenkolic acid with sulfur replaced by selenium and tellurium.

PubMed

Melnikov, Petr; Nascimento, Valter A; Silva, Anderson F; Consolo, Lourdes Z Z

2014-04-17

The comparative structural modeling of djenkolic acid and its derivatives containing selenium and tellurium in chalcogen sites (Ch=Se, Te) has provided detailed information about the bond lengths and bond angles, filling the gap in what we know about the structural characteristics of these aminoacids. The investigation using the molecular mechanics technique with good approximation confirmed the available information on X-ray refinements for the related compounds methionine and selenomethionine, as well as for an estimate made earlier for telluromethionine. It was shown that the Ch-C(3) and Ch-C(4) bond lengths grow in parallel with the increasing anionic radii. Although the distances C-C, C-O, and C-N are very similar, the geometry of conformers is quite different owing to the possibility of rotation about four carbon atoms, hence the remarkable variability observed in dihedral angles. It was shown that the compounds contain a rigid block with two Ch atoms connected through a methylene group. The standard program Gaussian 03 with graphical interface Gaussview 4.1.2 has proved to be satisfactory tool for the structural description of less-common bioactive compositions when direct X-ray results are absent.
Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.

PubMed

Perić-Hassler, Lovorka; Hansen, Halvor S; Baron, Riccardo; Hünenberger, Philippe H

2010-08-16

Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed. Copyright 2010 Elsevier Ltd. All rights reserved.
Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.

PubMed

Robertson, Michael J; Tirado-Rives, Julian; Jorgensen, William L

2015-07-14

The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.
Synthesis, structural characterization, and DFT calculations of 3-buthyl-4-(3-methyl-3-mesitylcyclobut-1-yl)-1,3-thiazole-2(3H)-thione

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

Şen, B.; Barim, E.; Kirilmis, C.

2016-03-15

The title compound, C{sub 21}H{sub 29}NS{sub 2}, has been synthesized and its crystal structure has been determined from single crystal X-ray diffraction data. Crystals are monoclinic, a = 11.4923(8), b = 13.1842(7), c = 14.6583(8) Å, β = 109.983(6)°, sp. gr. P2{sub 1}/c, Z = 4. Mesityl and thiazole groups are in cis positions with respect to the cyclobutane ring. The cyclobutane ring is puckered, with a dihedral angle of 26.6(2)° between the two three-atom planes. The crystal structure involves one weak intermolecular C–H···S hydrogen-bond. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G(d,more » p) basis set in ground state. Geometric parameters (bond lengths, bond angles and torsion angles) and vibrational assignments have been calculated theoretically and compared with the experimental data.« less
Conduction Properties of KcsA Measured Using Brownian Dynamics with Flexible Carbonyl Groups in the Selectivity Filter

PubMed Central

Chung, Shin-Ho; Corry, Ben

2007-01-01

In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to change in response to the forces acting upon them. By systematically changing the coefficients of bond stretching and of angle bending, the carbon and oxygen atoms can be made to fluctuate from their fixed positions by varying mean distances. We show that incorporating carbonyl motion in this way does not alter the mechanism of ion conduction and only has a small influence on the computed current. The slope conductance of the channel increases by ∼25% when the root mean-square fluctuations of the carbonyl groups are increased from 0.01 to 0.61 Å. The energy profiles and the number of resident ions in the channel remain unchanged. The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels. PMID:17434934
Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter.

PubMed

Chung, Shin-Ho; Corry, Ben

2007-07-01

In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to change in response to the forces acting upon them. By systematically changing the coefficients of bond stretching and of angle bending, the carbon and oxygen atoms can be made to fluctuate from their fixed positions by varying mean distances. We show that incorporating carbonyl motion in this way does not alter the mechanism of ion conduction and only has a small influence on the computed current. The slope conductance of the channel increases by approximately 25% when the root mean-square fluctuations of the carbonyl groups are increased from 0.01 to 0.61 A. The energy profiles and the number of resident ions in the channel remain unchanged. The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels.
2,4,8,10,13-Pentamethyl-6-phenyl-13,14-dihydro-12H-6λ5-dibenzo[d,i][1,3,7,2]dioxazaphosphecin-6-thione

PubMed Central

Krishnaiah, M.; Babu, V.H.H. Surendra; Sankar, A. Uma Ravi; Raju, C. Naga; Kant, Rajni

2010-01-01

In the title compound, C25H28NO2PS, the cyclodecene ring exhibits a crown conformation. The two dimethylbenzene rings which are fused symmetrically on either side of the ten-membered ring, make dihedral angles of 20.2 (1) and 18.0 (1)°. The phenyl ring substituted at P is perpendicular to the heterocyclic ring, making a dihedral angle of 88.4 (1)°. The crystal structure is stabilized by very weak intramolecular C—H⋯O hydrogen bonding. PMID:21580010
3-Ethyl-5-(4-methoxyphenoxy)-2-(pyridin-4-yl)-3H-imidazo[4,5-b]pyridine

PubMed Central

Ranjith, S.; SubbiahPandi, A.; Suresh, A. D.; Pitchumani, K.

2011-01-01

In the title compound, C20H18N4O2, the imidazopyridine fused ring system is almost perpendicular to the benzene ring [dihedral angle = 87.6 (5)°]. The pyridine ring makes a dihedral angle of 35.5 (5)° with the mean plane of the imidazopyridine fragment. The crystal structure is stabilized by an aromatic π–π stacking interaction between the phenyl rings of neighbouring molecules [centroid–centroid distance = 3.772 (2) Å, interplanar distance = 3.546 (2) Å and slippage = 1.286 (2) Å]. PMID:21837144
3-(4-Hydroxyphenyl)-1,5-bis(pyridin-2-yl)pentane-1,5-dione

PubMed Central

Pan, Lixia; Shi, Huaduan; Ma, Zhen

2013-01-01

In the title molecule, C21H18N2O3, the pyridine rings make a dihedral angle of 13.1 (1)°. The phenyl ring is approximately perpendicular to both of them, forming dihedral angles of 87.4 (1)and 81.9 (1)°. In the crystal, pairs of O—H⋯N hydrogen bonds link the molecules into centrosymmetric dimers. Additional C—H⋯O, π–π [centroid–centroid distance = 3.971 (2) Å] and C—H⋯π interactions consolidate the dimers into a three-dimensional network. PMID:24098256
N-(3-Chloro-1-methyl-1H-indazol-5-yl)-4-methylbenzenesulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Amiri, Ouafa; Saadi, Mohamed; El Ammari, Lahcen

2014-01-01

The asymmetric unit of the title compound, C15H14ClN3O2S, contains two independent molecules showing different conformations: in one molecule, the indazole ring system makes a dihedral angle of 51.5 (1)° with the benzene ring whereas in the other, the indazole unit is almost perpendicular to the benzene ring [dihedral angle 77.7 (1)°]. In the crystal, the molecules are linked by N—H⋯N and N—H⋯O hydrogen bonds, forming a set of four molecules linked in pairs about an inversion centre. PMID:24764895
5-Amino-7-(4-bromophenyl)-3,7-dihydro-2H-thieno[3,2-b]pyran-6-carbonitrile 1,1-dioxide

PubMed Central

Yu, Chen-Xia; Feng, Xiao-Dong; Jiang, Bei; Wang, Cui-Hua; Yao, Chang-Sheng

2010-01-01

In the title compound, C14H11BrN2O3S, the 2,3-dihydrothiophene ring is almost planar [maximum deviation = 0.006 (1) Å]. The pyran ring is in an envelope conformation [puckering parameters Q = 0.115 (2) Å, θ = 77.5 (10), ϕ = 172.9 (10)°]. The pyran and phenyl rings are approximately perpendicular, making a dihedral angle of −76.4 (2)°. The crystal packing is stabilized by intermolecular N—H⋯O hydrogen bonds, with the sulfone O atoms acting as acceptors. PMID:21579705
(E)-1-[2-Hy-droxy-4,6-bis-(meth-oxy-meth-oxy)phen-yl]-3-phenyl-prop-2-en-1-one.

PubMed

Niu, Chao; Liu, Y Q; He, Y W; Aisa, H A

2013-05-01

The title compound, C19H20O6, consists of a tetra-substituted benzene ring with one substituent being an α,β-unsaturated cinnamoyl group, which forms an extended conjugated system in the mol-ecule. In addition, two meth-oxy-meth-oxy and one hy-droxy group are bonded to the central benzene ring. The dihedral angle between eh rings is 10.22 (10)°. An intra-molecular hydrogen bond is observed between the hy-droxy group and the carbonyl O atom. One of the meth-oxy-meth-oxy substituents is conformationally disordered over two sets of sites with site-occupation factors of 0.831 (3) and 0.169 (3).
Bis(2,1,3-benzoselenadiazole-κN)dibromidocopper(II)

PubMed Central

Fun, Hoong-Kun; Goh, Jia Hao; Maity, Annada C.; Goswami, Shyamaprosad

2011-01-01

In the title complex, [CuBr2(C6H4N2Se)2], the CuII ion is tetracoordinated by two bromide anions and two N atoms in a distorted square-planar geometry. The two essentially planar 2,1,3-benzoselenadiazole ligands [maximum deviations = 0.012 (2) and 0.030 (2) Å] are approximately coplanar [dihedral angle = 6.14 (6)°]. In the crystal, short intermolecular Se⋯Br, Se⋯N and N⋯N interactions are observed. These short interactions and intermolecular C—H⋯Br hydrogen bonds link the complex molecules into two-dimensional arrays parallel to the ac plane. PMID:21522854
Quantum chemical determination of Young's modulus of lignin. Calculations on a beta-O-4' model compound.

PubMed

Elder, Thomas

2007-11-01

The calculation of Young's modulus of lignin has been examined by subjecting a dimeric model compound to strain, coupled with the determination of energy and stress. The computational results, derived from quantum chemical calculations, are in agreement with available experimental results. Changes in geometry indicate that modifications in dihedral angles occur in response to linear strain. At larger levels of strain, bond rupture is evidenced by abrupt changes in energy, structure, and charge. Based on the current calculations, the bond scission may be occurring through a homolytic reaction between aliphatic carbon atoms. These results may have implications in the reactivity of lignin especially when subjected to processing methods that place large mechanical forces on the structure.
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

PubMed Central

Davis, Ian W.; Leaver-Fay, Andrew; Chen, Vincent B.; Block, Jeremy N.; Kapral, Gary J.; Wang, Xueyi; Murray, Laura W.; Arendall, W. Bryan; Snoeyink, Jack; Richardson, Jane S.; Richardson, David C.

2007-01-01

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu. PMID:17452350
Bis{2-methoxy-6-[tris(hydroxymethyl)methyliminomethyl]phenolato-κ3 O,N,O′}manganese(II) dimethanol solvate hemihydrate

PubMed Central

Zhang, Xiutang; Wei, Peihai; Dou, Jianmin; Li, Bin; Hu, Bo

2009-01-01

In the title complex, [Mn(C12H16NO5)2]·2CH3OH·0.5H2O, the MnII atom has a distorted octahedral coordination geometry in which two N atoms from two 6-methoxy-2-[tris(hydroxymethyl)methyliminomethyl]phenolate ligands adopt a trans arrangement. The Mn—O(H) bonds (mean length 2.134 Å) are significantly longer than the Mn—O and Mn—N bonds (mean length 2.011 and 2.027 Å, respectively), and the dihedral angle between the mean planes through the aromatic rings of the two ligands is 76.8 (1)°. A complex network of O—H⋯O hydrogen bonds is formed between the complexes and the uncoordinated methanol and water molecules. The C and O atoms of one C—OH group are disordered with equal occupancies. PMID:21582076
Atomic torsional modal analysis for high-resolution proteins.

PubMed

Tirion, Monique M; ben-Avraham, Daniel

2015-03-01

We introduce a formulation for normal mode analyses of globular proteins that significantly improves on an earlier one-parameter formulation [M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996)] that characterized the slow modes associated with protein data bank structures. Here we develop that empirical potential function that is minimized at the outset to include two features essential to reproduce the eigenspectra and associated density of states in the 0 to 300cm-1 frequency range, not merely the slow modes. First, introduction of preferred dihedral-angle configurations via use of torsional stiffness constants eliminates anomalous dispersion characteristics due to insufficiently bound surface side chains and helps fix the spectrum thin tail frequencies (100-300cm-1). Second, we take into account the atomic identities and the distance of separation of all pairwise interactions, improving the spectrum distribution in the 20 to 300cm-1 range. With these modifications, not only does the spectrum reproduce that of full atomic potentials, but we obtain stable reliable eigenmodes for the slow modes and over a wide range of frequencies.

Measurement of the Static Stability and Control and the Damping Derivatives of a 0.13-Scale Model of the Convair XFY-1 Airplane, TED No. NACA DE 368

NASA Technical Reports Server (NTRS)

Johnson, Joseph L.

1954-01-01

An investigation has been conducted to determine the static stability and control and damping in roll and yaw of a 0.13-scale model of the Convair XFY-1 airplane with propellers off from 0 deg to 90 deg angle of attack. The tests showed that a slightly unstable pitch-up tendency occurred simultaneously with a break in the normal-force curve in the angle-of-attack range from about 27 deg to 36 deg. The top vertical tail contributed positive values of static directional stability and effective dihedral up to an angle of attack of about 35 deg. The bottom tail contributed positive values of static directional stability but negative values of effective dihedral throughout the angle-of-attack range. Effectiveness of the control surfaces decreased to very low values at the high angles of attack, The model had positive damping in yaw and damping in roll about the body axes over the angle-of-attack range but the damping in yaw decreased to about zero at 90 deg angle of attack.
The calculation of lateral stability with free controls

NASA Technical Reports Server (NTRS)

Mathias, Gotthold

1934-01-01

The discussion of the structural methods for obtaining lateral stability discloses the remarkable influence of the constant fuselage and wing proportions to the yawing moments. For the effectiveness of modifications in vertical tail surfaces and tail length, these quotas - little observed heretofore, in this connection - are decisive. This also applies to the amount of dihedral of the wing with regard to the roll stability of the complete wing already existing without angle of the dihedral.
Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?

PubMed Central

Moradi, Mahmoud; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2012-01-01

We have characterized the conformational ensembles of polyglutamine peptides of various lengths (ranging from to ), both with and without the presence of a C-terminal polyproline hexapeptide. For this, we used state-of-the-art molecular dynamics simulations combined with a novel statistical analysis to characterize the various properties of the backbone dihedral angles and secondary structural motifs of the glutamine residues. For (i.e., just above the pathological length for Huntington's disease), the equilibrium conformations of the monomer consist primarily of disordered, compact structures with non-negligible -helical and turn content. We also observed a relatively small population of extended structures suitable for forming aggregates including - and -strands, and - and -hairpins. Most importantly, for we find that there exists a long-range correlation (ranging for at least residues) among the backbone dihedral angles of the Q residues. For polyglutamine peptides below the pathological length, the population of the extended strands and hairpins is considerably smaller, and the correlations are short-range (at most residues apart). Adding a C-terminal hexaproline to suppresses both the population of these rare motifs and the long-range correlation of the dihedral angles. We argue that the long-range correlation of the polyglutamine homopeptide, along with the presence of these rare motifs, could be responsible for its aggregation phenomena. PMID:22577357
The Physical Basis for the Head-to-Tail Rule that Excludes Most Fullerene Cages from Self-Assembly☆

PubMed Central

Schein, Stan; Sands-Kidner, Michelle; Friedrich, Tara

2008-01-01

Abstract In the companion article, we proposed that fullerene cages with head-to-tail dihedral angle discrepancies do not self-assemble. Here we show why. If an edge abuts a pentagon at one end and a hexagon at the other, the dihedral angle about the edge increases, producing a dihedral angle discrepancy (DAD) vector. The DADs about all five/six edges of a central pentagonal/hexagonal face are determined by the identities—pentagon or hexagon—of its five/six surrounding faces. Each “Ring”—central face plus specific surrounding faces—may have zero, two, or four edges with DAD. In most Rings, the nonplanarity induced by DADs is shared among surrounding faces. However, in a Ring that has DADs arranged head of one to tail of another, the nonplanarity cannot be shared, so some surrounding faces would be especially nonplanar. Because the head-to-tail exclusion rule is an implicit geometric constraint, the rule may operate either by imposing a kinetic barrier that prevents assembly of certain Rings or by imposing an energy cost that makes those Rings unlikely to last in an equilibrium circumstance. Since Rings with head-to-tail DADs would be unlikely to self-assemble or last, fullerene cages with those Rings would be unlikely to self-assemble. PMID:17921208
Gauche effect in 1,2-difluoroethane. Hyperconjugation, bent bonds, steric repulsion.

PubMed

Goodman, Lionel; Gu, Hongbing; Pophristic, Vojislava

2005-02-17

Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.
The effect of canard leading edge sweep and dihedral angle on the longitudinal and lateral aerodynamic characteristic of a close-coupled canard-wing configuration

NASA Technical Reports Server (NTRS)

Gloss, B. B.

1974-01-01

A generalized wind-tunnel model, with canard and wing planforms typical of highly maneuverable aircraft, was tested in the Langley high-speed 7- by 10-foot tunnel at a Mach number of 0.30. The test was conducted in order to determine the effects of canard sweep and canard dihedral on canard-wing interference at high angles of attack. In general, the effect of canard sweep on lift is small up to an angle of attack of 16 deg. However, for angles of attack greater than 16 deg, an increase in the canard sweep results in an increase in lift developed by the canard when the canard is above or in the wing chord plane. This increased lift results in a lift increase for the total configuration for the canard above the wing chord plane. For the canard in the wing chord plane, the increased canard lift is partially lost by increased interference on the wing.
Crystal structure of 4-fluoro-N-[2-(4-fluoro-benzo-yl)hydra-zine-1-carbono-thio-yl]benzamide.

PubMed

Firdausiah, Syadza; Salleh Huddin, Ameera Aqeela; Hasbullah, Siti Aishah; Yamin, Bohari M; Yusoff, Siti Fairus M

2014-09-01

In the title compound, C15H11F2N3O2S, the dihedral angle between the fluoro-benzene rings is 88.43 (10)° and that between the central semithiocarbazide grouping is 47.00 (11)°. The dihedral angle between the amide group and attached fluoro-benzene ring is 50.52 (11)°; the equivalent angle between the carbonyl-thio-amide group and its attached ring is 12.98 (10)°. The major twists in the mol-ecule occur about the C-N-N-C bonds [torsion angle = -138.7 (2)°] and the Car-Car-C-N (ar = aromatic) bonds [-132.0 (2)°]. An intra-molecular N-H⋯O hydrogen bond occurs, which generates an S(6) ring. In the crystal, the mol-ecules are linked by N-H⋯O and N-H⋯S hydrogen bonds, generating (001) sheets. Weak C-H⋯O and C-H⋯F inter-actions are also observed.
Equilibrium configurations of the conducting liquid surface in a nonuniform electric field

NASA Astrophysics Data System (ADS)

Zubarev, N. M.; Zubareva, O. V.

2011-01-01

Possible equilibrium configurations of the free surface of a conducting liquid deformed by a nonuniform external electric field are investigated. The liquid rests on an electrode that has the shape of a dihedral angle formed by two intersecting equipotential half-planes (conducting wedge). It is assumed that the problem has plane symmetry: the surface is invariant under shift along the edge of the dihedral angle. A one-parametric family of exact solutions for the shape of the surface is found in which the opening angle of the region above the wedge serves as a parameter. The solutions are valid when the pressure difference between the inside and outside of the liquid is zero. For an arbitrary pressure difference, approximate solutions to the problem are constructed and it is demonstrated the approximation error is small. It is found that, when the potential difference exceeds a certain threshold value, equilibrium solutions are absent. In this case, the region occupied by the liquid disintegrates, the disintegration scenario depending on the opening angle.
Crystal structures of three indole derivatives: 3-ethnyl-2-methyl-1-phenylsulfonyl-1H-indole, 4-phenylsulfonyl-3H,4H-cyclopenta[b]indol-1(2H)-one and 1-{2-[(E)-2-(5-chloro-2-nitrophenyl)ethenyl]-1-phenylsulfonyl-1H-indol-3-yl}ethan-1-one chloroform monosolvate

PubMed Central

Gopinath, S.; Sethusankar, K.; Ramalingam, Bose Muthu; Mohanakrishnan, Arasambattu K.

2015-01-01

The title compounds, C17H13NO2S, (I), C17H13NO3S, (II), and C24H17ClN2O5S·CHCl3, (III), are indole derivatives. Compounds (I) and (II) crystalize with two independent molecules in the asymmetric unit. The indole ring systems in all three structures deviate only slightly from planarity, with dihedral angles between the planes of the pyrrole and benzene rings spanning the tight range 0.20 (9)–1.65 (9)°. These indole ring systems, in turn, are almost orthogonal to the phenylsulfonyl rings [range of dihedral angles between mean planes = 77.21 (8)–89.26 (8)°]. In the three compounds, the molecular structure is stabilized by intramolecular C—H⋯O hydrogen bonds, generating S(6) ring motifs with the sulfone O atom. In compounds (I) and (II), the two independent molecules are linked by C—H⋯O hydrogen bonds and C—H⋯π interactions, while in compound (III), the molecules are linked by C—H⋯O hydrogen bonds, generating R 2 2(22) inversion dimers. PMID:26396842
B-spline tight frame based force matching method

NASA Astrophysics Data System (ADS)

Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei

2018-06-01

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.
Diethyl 2,2′-(ethane-1,2-diyldioxy)dibenzoate

PubMed Central

Shi, Huaduan; Qin, Haisha; Ma, Zhen

2014-01-01

The molecular title compound, C20H22O6, was obtained by the reaction of ethyl 2-hydroxybenzoate with 1,2-dichloroethane. The molecule lies on a twofold rotation axis which passes through the middle of the central ethylene bridge. This group exhibits a gauche conformation with the corresponding O—C—C—O torsion angle being 73.2 (2)°. The C atoms of the carboxyl group, the aryl and the O—CH2 group are coplanar, with an r.m.s. deviation of 0.01 Å. The two aryl rings form a dihedral angle of 67.94 (4)°. The ester ethyl group is disordered over two sets of sites with an occupancy ratio of 0.59 (2):0.41 (2). The crystal packing is dominated by van der Waals forces. PMID:24860360
Investigation of Aerodynamic Capabilities of Flying Fish in Gliding Flight

NASA Astrophysics Data System (ADS)

Park, H.; Choi, H.

In the present study, we experimentally investigate the aerodynamic capabilities of flying fish. We consider four different flying fish models, which are darkedged-wing flying fishes stuffed in actual gliding posture. Some morphological parameters of flying fish such as lateral dihedral angle of pectoral fins, incidence angles of pectoral and pelvic fins are considered to examine their effect on the aerodynamic performance. We directly measure the aerodynamic properties (lift, drag, and pitching moment) for different morphological parameters of flying fish models. For the present flying fish models, the maximum lift coefficient and lift-to-drag ratio are similar to those of medium-sized birds such as the vulture, nighthawk and petrel. The pectoral fins are found to enhance the lift-to-drag ratio and the longitudinal static stability of gliding flight. On the other hand, the lift coefficient and lift-to-drag ratio decrease with increasing lateral dihedral angle of pectoral fins.
The effect of wing dihedral and section suction distribution on vortex bursting

NASA Technical Reports Server (NTRS)

Washburn, K. E.; Gloss, B. B.

1975-01-01

Eleven semi-span wing models were tested in the 1/8-scale model of the Langley V/STOL tunnel to qualitatively study vortex bursting. Flow visualization was achieved by using helium filled soap bubbles introduced upstream of the model. The angle of attack range was from 0 deg to 45 deg. The results show that the vortex is unstable, that is, the bursting point location is not fixed at a given angle of attack but moves within certain bounds. Upstream of the trailing edge, the bursting point location has a range of two inches; downstream, the range is about six inches. Anhedral and dihedral appear to have an insignificant effect on the vortex and its bursting point location. Altering the section suction distribution by improving the triangularity generally increases the angle of attack at which vortex bursting occurs at the trailing edge.
Aerodynamics, aeroelasticity, and stability of hang gliders. Experimental results. [Ames 7- by 10-ft wind tunnel tests

NASA Technical Reports Server (NTRS)

Kroo, I. M.

1981-01-01

One-fifth-scale models of three basic ultralight glider designs were constructed to simulate the elastic properties of full scale gliders and were tested at Reynolds numbers close to full scale values. Twenty-four minor modifications were made to the basic configurations in order to evaluate the effects of twist, reflex, dihedral, and various stability enhancement devices. Longitudinal and lateral data were obtained at several speeds through an angle of attack range of -30 deg to +45 deg with sideslip angles of up to 20 deg. The importance of vertical center of gravity displacement is discussed. Lateral data indicate that effective dihedral is lost at low angles of attack for nearly all of the configurations tested. Drag data suggest that lift-dependent viscous drag is a large part of the glider's total drag as is expected for thin, cambered sections at these relatively low Reynolds numbers.
Three-Dimensional Mapping of Microenvironmental Control of Methyl Rotational Barriers

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

Hembree, William I; Baudry, Jerome Y

2011-01-01

Sterical (van der Waals-induced) rotational barriers of methyl groups are investigated theoretically, using ab initio and empirical force field calculations, for various three-dimensional microenvironmental conditions around the methyl group rotator of a model neopentane molecule. The destabilization (reducing methyl rotational barriers) or stabilization (increasing methyl rotational barriers) of the staggered conformation of the methyl rotator depends on a combination of microenvironmental contributions from (i) the number of atoms around the rotator, (ii) the distance between the rotator and the microenvironmental atoms, and (iii) the dihedral angle between the stator, rotator, and molecular environment around the rotator. These geometrical criteria combinemore » their respective effects in a linearly additive fashion, with no apparent cooperative effects, and their combination in space around a rotator may increase, decrease, or leave the rotator s rotational barrier unmodified. This is exemplified in a geometrical analysis of the alanine dipeptide crystal where microenvironmental effects on methyl rotators barrier of rotation fit the geometrical mapping described in the neopentane model.« less
Envisaging Structural Insight of a Terminally Protected Proline Dipeptide by Raman Spectroscopy and Density Functional Theory Analyses.

PubMed

Das, Supriya; Pal, Uttam; Chatterjee, Moumita; Pramanik, Sumit Kumar; Banerji, Biswadip; Maiti, Nakul C

2016-12-15

The proline residue in a protein sequence generates constraints to its secondary structure as the associated torsion angles become a part of the heterocyclic ring. It becomes more significant when two consecutive proline residues link via amide linkage and produce additional configurational constraint to a protein's folding and stability. In the current manuscript we have illustrated conformation preference of a novel dipeptide, (R)-tert-butyl 2-((S)-2-(methoxycarbonyl)pyrrolidine-1-carbonyl)pyrrolidine-1-carboxylate. The dipeptide crystallized in the orthorhombic crystalline state and produced rod-shaped macroscopic material. The analysis of the crystal coordinates showed dihedral angles (φ, ψ) of the interlinked amide groups as (+72°, -147°) and the dihedral angles (φ, ψ) produced with the next carbonyl were (-68°, +151°), indicating polyglycine II (PGII) and polyproline II (PPII)-like helix states at the N- and C-terminals, respectively. These two states, PGII and PPII, are mirror image configurations and are expected to produce similar vibration bands from the associated carbonyl groups. However, the unique atomic arrangement in the molecule produces three carbonyl groups and one of them was very specific, being part of the main peptide linkage that connects both the pyrrolidine rings. The carbonyl group in the peptide bond exhibited a Raman vibration frequency at ∼1642 cm -1 and is considered a signatory Raman marker band for the peptide bond linking two heterochiral proline residues. The carbonyl group (t-Boc) at the N-terminal of the peptide showed a characteristic vibration at ∼1685 cm -1 and the C-terminal carbonyl group as a part of the ester showed a vibration signature at a significantly high frequency (1746 cm -1 ). Conformation analyses performed with density functional theory (DFT) calculations depicted that the dipeptide was stabilized in vacuum with dihedral angles (+72°, -154°) and (-72°, +151°) at the N- and C-terminals, respectively. Molecular dynamics (MD) simulation also showed that the peptide conformation having dihedral angles around (+75°, -150°) and (-75°, +150°) at the N- and C-terminals, respectively, was reasonably stable in water. Due to unique absence of the amide N-H, the peptide was ineffective in forming any intramolecular hydrogen bonding. MD investigation, however, revealed an intermolecular hydrogen bonding interaction with the water molecules, leading to its stability in aqueous solution. Metadynamics simulation analysis of the dipeptide in water also supported the PGII-PPII-like conformation at the N- and C-terminals, respectively, as the energetically stable conformation among the other possible combinations of conformations. The possible electronic transitions along with the HOMO-LUMO analysis further depicted the stability of the dipeptide in water and their possible absorption pattern. Time-dependent density functional theory (TDDFT) analysis showed strong negative rotatory strength of the dipeptide around 210 nm in water and acetonitrile, and it could be the source of experimentally observed high-amplitude negative absorption in the circular dichroism (CD) spectra around 200-203 nm. The very weak positive band (signature) in the region at ∼228 nm in CD spectra could also be correlated to the positive rotatory strength at 228 nm observed in ECD. To test the effect of such a dipeptide on a living cell, an MTT assay was performed and the result indicated no cytotoxic effect toward human hepatocellular carcinoma Hep G2 cancer cell lines.
Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures

PubMed Central

2010-01-01

Background β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. Results We have developed a novel method that predicts β-turns and their types using information from multiple sequence alignments, predicted secondary structures and, for the first time, predicted dihedral angles. Our method uses support vector machines, a supervised classification technique, and is trained and tested on three established datasets of 426, 547 and 823 protein chains. We achieve a Matthews correlation coefficient of up to 0.49, when predicting the location of β-turns, the highest reported value to date. Moreover, the additional dihedral information improves the prediction of β-turn types I, II, IV, VIII and "non-specific", achieving correlation coefficients up to 0.39, 0.33, 0.27, 0.14 and 0.38, respectively. Our results are more accurate than other methods. Conclusions We have created an accurate predictor of β-turns and their types. Our method, called DEBT, is available online at http://comp.chem.nottingham.ac.uk/debt/. PMID:20673368
Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures.

PubMed

Kountouris, Petros; Hirst, Jonathan D

2010-07-31

Beta-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. We have developed a novel method that predicts beta-turns and their types using information from multiple sequence alignments, predicted secondary structures and, for the first time, predicted dihedral angles. Our method uses support vector machines, a supervised classification technique, and is trained and tested on three established datasets of 426, 547 and 823 protein chains. We achieve a Matthews correlation coefficient of up to 0.49, when predicting the location of beta-turns, the highest reported value to date. Moreover, the additional dihedral information improves the prediction of beta-turn types I, II, IV, VIII and "non-specific", achieving correlation coefficients up to 0.39, 0.33, 0.27, 0.14 and 0.38, respectively. Our results are more accurate than other methods. We have created an accurate predictor of beta-turns and their types. Our method, called DEBT, is available online at http://comp.chem.nottingham.ac.uk/debt/.
Crystal structure of 1,3-bis{[4-(acetylsulfanyl)phenyl]ethynyl}azulene

PubMed Central

Förster, Sebastian; Seichter, Wilhelm; Weber, Edwin

2015-01-01

In the title compound, C30H20O2S2, the dihedral angles between the central azulene ring system (r.m.s. deviation = 0.039 Å) and the pendant benzene rings are 28.96 (7) and 55.15 (7)°. The dihedral angles between the benzene rings and their attached acetylsulfanyl groups are 59.60 (10) and 84.79 (10)°. The expected π–π stacking interactions are not observed in the crystal structure; instead, the packing features C—H⋯O hydrogen bonds, which link the molecules into C(12) [010] chains, which are supported by weak C—H⋯π contacts. PMID:26870518
(2E)-3-(4-Cyanophenyl)-1-(4,4′′-difluoro-5′-methoxy-1,1′:3′,1′′-terphenyl-4′-yl)prop-2-en-1-one

PubMed Central

Fun, Hoong-Kun; Loh, Wan-Sin; Samshuddin, S.; Narayana, B.; Sarojini, B. K.

2012-01-01

In the title compound, C29H19F2NO2, the central benzene ring forms a dihedral angle of 56.92 (12)° with the cyanobenzene ring and dihedral angles of 40.91 (12) and 44.76 (12)° with the two fluorobenzene rings. In the crystal, C—H⋯O and C—H⋯F hydrogen bonds link the molecules into sheets lying parallel to the ab plane. The crystal packing also features C—H⋯π interactions involving the central benzene ring. PMID:22719638

Crystal structure of 8-hy-droxy-quinolin-ium 2-carboxy-6-nitro-benzoate mono-hydrate.

PubMed

Divya Bharathi, M; Ahila, G; Mohana, J; Chakkaravarthi, G; Anbalagan, G

2015-04-01

In the title hydrated salt, C9H8NO(+)·C8H4NO6 (-)·H2O, the deprotonated carboxyl-ate group is almost normal to its attached benzene ring [dihedral angle = 83.56 (8)°], whereas the protonated carboxyl-ate group is close to parallel [dihedral angle = 24.56 (9)°]. In the crystal, the components are linked by N-H⋯O and O-H⋯O hydrogen bonds, generating [001] chains. The packing is consolidated by C-H⋯O and π-π [centroid-to-centroid distances = 3.6408 (9) and 3.6507 (9) Å] inter-actions, which result in a three-dimensional network.
An ab initio study of the conformational energy map of acetylcholine

NASA Astrophysics Data System (ADS)

Segall, M. D.; Payne, M. C.; Boyes, R. N.

An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans , gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.
Ethyl 2-(1,2,3,4-tetrahydrospiro[carbazole-3,2′-[1,3]dioxolan]-9-yl)acetate

PubMed Central

Löffler, Philipp M. G.; Ulven, Trond; Bond, Andrew D.

2009-01-01

In the title compound, C18H21NO4, the hydrogenated six-membered ring of the carbazole unit adopts a half-chair conformation. The dioxolane ring and ethylacetate substituent point to opposite sides of the carbazole plane. The ethylacetate substituent adopts an essentially fully extended conformation, and its mean plane forms a dihedral angle of 83.8 (1)° with respect to the carbazole mean plane. The molecules are arranged into stacks in which the carbazole planes form a dihedral angle of 4.4 (1)° and have an approximate interplanar separation of 3.6 Å. PMID:21582427
Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor

NASA Astrophysics Data System (ADS)

Brooks, Bernard; Karplus, Martin

1983-11-01

A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibitor in the full conformational space of the molecule (1,740 degrees of freedom); that is, all bond lengths and angles, as well as dihedral angles, are included for the 580-atom system consisting of all heavy atoms and polar hydrogens. The heavy-atom frequency spectrum shows a dense distribution between 3 and 1,800 cm-1, with 350 modes below 216 cm-1. Most of the low-frequency modes, of which many have significant anharmonic character, are found to be delocalized over the protein. The root-mean-square amplitudes of the atomic fluctuations are calculated at 300 K from the normal modes and compared with those obtained from a solution molecular dynamics simulation based on the same potential function; very good agreement is obtained for the variation in the main-chain fluctuations as a function of residue number, though larger differences occur for the side chains. The fluctuations are generally, though not always, dominated by frequencies below 30 cm-1, in accord with the results of the dynamics simulation. The vibrational contributions to the thermodynamic properties of the protein are calculated as a function of temperature; the effects of perturbations on the spectrum, suggested for ligand or substrate binding, are examined. The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.
Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

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

2005-06-01

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

PubMed

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

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.
14 CFR 25.427 - Unsymmetrical loads.

Code of Federal Regulations, 2011 CFR

2011-01-01

... STANDARDS: TRANSPORT CATEGORY AIRPLANES Structure Control Surface and System Loads § 25.427 Unsymmetrical... tail surfaces have dihedral angles greater than plus or minus 10 degrees, or are supported by the... specified in § 25.341(a) acting in any orientation at right angles to the flight path. (d) Unsymmetrical...
Interpolation schemes for peptide rearrangements.

PubMed

Bauer, Marianne S; Strodel, Birgit; Fejer, Szilard N; Koslover, Elena F; Wales, David J

2010-02-07

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.
4-{2-[2-(4-Formyl-phen-oxy)eth-oxy]eth-oxy}benzaldehyde.

PubMed

Ma, Zhen; Cao, Yiqun

2011-06-01

The title compound, C(18)H(18)O(5), was obtained by the reaction of 4-hy-droxy-benzaldehyde with bis-(2,2-dichloro-eth-yl) ether in dimethyl-formamide. In the crystal, the mol-ecule lies on a twofold rotation axis that passes through the central O atom of the aliphatic chain, thus leading to one half-mol-ecule being present per asymmetric unit. The carbonyl, aryl and O-CH(2)-CH(2) groups are almost coplanar, with an r.m.s. deviation of 0.030 Å. The aromatic rings are approximately perpendicular to each other, forming a dihedral angle of 78.31 sh;H⋯O hydrogen bonds and C-H⋯π inter-actions help to consolidate the three-dimensional network.
Crystal structure of 2-(1,3-dioxoindan-2-yl)iso-quinoline-1,3,4-trione.

PubMed

Ghalib, Raza Murad; Chidan Kumar, C S; Hashim, Rokiah; Sulaiman, Othman; Fun, Hoong-Kun

2015-01-01

In the title iso-quinoline-1,3,4-trione derivative, C18H9NO5, the five-membered ring of the indane fragment adopts an envelope conformation with the nitro-gen-substituted C atom being the flap. The planes of the indane benzene ring and the iso-quinoline-1,3,4-trione ring make a dihedral angle of 82.06 (6)°. In the crystal, mol-ecules are linked into chains extending along the bc plane via C-H⋯O hydrogen-bonding inter-actions, enclosing R 2 (2)(8) and R 2 (2)(10) loops. The chains are further connected by π-π stacking inter-ations, with centroid-to-centroid distances of 3.9050 (7) Å, forming layers parallel to the b axis.
Crystal and molecular structure of (2Z,5Z)-3-(2-methoxyphenyl)-2-[(2-methoxyphenyl)imino]-5-(4-nitrobenzylidene)thiazolidin-4-one

PubMed Central

Djafri, Ahmed; Daran, Jean-Claude; Djafri, Ayada

2017-01-01

In the title compound, C24H19N3O5S, the thiazole ring (r.m.s. deviation = 0.012 Å) displays a planar geometry and is surrounded by three fragments, two methoxyphenyl and one nitrophenyl. The thiazole ring is almost in the same plane as the nitrophenyl ring, making a dihedral angle of 20.92 (6)°. The two methoxyphenyl groups are perpendicular to the thiazole ring [dihedral angles of 79.29 (6) and 71.31 (7)° and make a dihedral angle of 68.59 (7)°. The molecule exists in an Z,Z conformation with respect to the C=N imine bond. In the crystal, a series of C—H⋯N, C—H⋯O and C—H⋯S hydrogen bonds, augmented by several π–π(ring) interactions, produce a three-dimensional architecture of molecules stacked along the b-axis direction. The experimentally derived structure is compered with that calculated theoretically using DFT(B3YLP) methods. PMID:28435709
Control effectiveness and tip-fin dihedral effects for the HL-20 lifting-body configuration at Mach numbers from 1.6 to 4.5

NASA Technical Reports Server (NTRS)

Cruz, Christopher I.; Ware, George M.

1995-01-01

Wind tunnel tests were made with a scale model of the HL-20 in the Langley Unitary Plan Wind Tunnel. Pitch control was investigated by deflecting the elevon surfaces on the outboard fins and body flaps on the fuselage. Yaw control tests were made with the all movable center fin deflected 5 deg. Almost full negative body flap deflection (-30 deg) was required to trim the HL-20 (moment reference center at 0.54-percent body length from nose) to positive values of life in the Mach number range from 1.6 to 2.5. Elevons were twice as effective as body flaps as a longitudinal trim device. The elevons were effective as a roll control, but because of tip-fin dihedral angle, produced about as much adverse yawing moment as rolling moment. The body flaps were less effective in producing rolling moment, but produced little adverse yawing moment. The yaw effectiveness of the all movable center fin was essentially constant over the angle-of-attack range at each Mach number. The value of yawing moment, however, was small. Center-fin deflection produced almost no rolling moments. The model was directionally unstable over most of the Mach number range with tip-fin dihedral angles less than the baseline value of 50 deg.
Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations.

PubMed

Tappura, K

2001-08-15

An adjustable-barrier dihedral angle potential was added as an extension to a novel, previously presented soft-core potential to study its contribution to the efficacy of the search of the conformational space in molecular dynamics. As opposed to the conventional soft-core potential functions, the leading principle in the design of the new soft-core potential, as well as of its extension, the soft-core and adjustable-barrier dihedral angle (SCADA) potential (referred as the SCADA potential), was to maintain the main equilibrium properties of the original force field. This qualifies the methods for a variety of a priori modeling problems without need for additional restraints typically required with the conventional soft-core potentials. In the present study, the different potential energy functions are applied to the problem of predicting loop conformations in proteins. Comparison of the performance of the soft-core and SCADA potential showed that the main hurdles for the efficient sampling of the conformational space of (loops in) proteins are related to the high-energy barriers caused by the Lennard-Jones and Coulombic energy terms, and not to the rotational barriers, although the conformational search can be further enhanced by lowering the rotational barriers of the dihedral angles. Finally, different evaluation methods were studied and a few promising criteria found to distinguish the near-native loop conformations from the wrong ones.
Crystal structure of azilsartan methyl ester ethyl acetate hemisolvate.

PubMed

Li, Zhengyi; Liu, Rong; Zhu, Meilan; Chen, Liang; Sun, Xiaoqiang

2015-02-01

The title compound, C26H22N4O5 (systematic name: methyl 2-eth-oxy-1-{4-[2-(5-oxo-4,5-di-hydro-1,2,4-oxa-diazol-3-yl)phenyl]benz-yl}-1H-1,3-benzo-diazole-7-carboxyl-ate ethyl acetate hemisolvate), was obtained via cyclization of methyl (Z)-2-eth-oxy-1-{(2'-(N'-hy-droxy-carbamimido-yl)-[1,1'-biphen-yl]-4-yl)meth-yl}-1H-benzo[d]imidazole-7-carboxyl-ate with diphen-yl carbonate. There are two independent mol-ecules (A and B) with different conformations and an ethyl acetate solvent mol-ecule in the asymmetric unit. In mol-ecule A, the dihedral angle between the benzene ring and its attached oxa-diazole ring is 59.36 (17); the dihedral angle between the benzene rings is 43.89 (15) and that between the benzene ring and its attached imidazole ring system is 80.06 (11)°. The corres-ponding dihedral angles in mol-ecule B are 58.45 (18), 50.73 (16) and 85.37 (10)°, respectively. The C-O-C-Cm (m = meth-yl) torsion angles for the eth-oxy side chains attached to the imidazole rings in mol-ecules A and B are 93.9 (3) and -174.6 (3)°, respectively. In the crystal, the components are linked by N-H⋯N and C-H⋯O hydrogen bonds, generating a three-dimensional network. Aromatic π-π stacking inter-actions [shortest centroid-centroid separation = 3.536 (3)Å] are also observed.
14 CFR 29.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2011 CFR

2011-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 23.1391 - Minimum intensities in the horizontal plane of position lights.

Code of Federal Regulations, 2012 CFR

2012-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white) 110° to...
14 CFR 29.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2013 CFR

2013-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 27.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2013 CFR

2013-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 10° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 25.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2014 CFR

2014-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 23.1391 - Minimum intensities in the horizontal plane of position lights.

Code of Federal Regulations, 2013 CFR

2013-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white) 110° to...

14 CFR 25.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2011 CFR

2011-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 0° to 10° 10° to 20° 20° to 110° 40 30 5 A (rear white...
14 CFR 29.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2014 CFR

2014-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 27.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2011 CFR

2011-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 10° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 25.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2013 CFR

2013-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 27.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2014 CFR

2014-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 10° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 23.1391 - Minimum intensities in the horizontal plane of position lights.

Code of Federal Regulations, 2014 CFR

2014-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white) 110° to...
14 CFR 27.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2012 CFR

2012-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 10° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 25.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2012 CFR

2012-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 0° to 10° 10° to 20° 20° to 110° 40 30 5 A (rear white...
14 CFR 29.1391 - Minimum intensities in the horizontal plane of forward and rear position lights.

Code of Federal Regulations, 2012 CFR

2012-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (forward red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white...
14 CFR 23.1391 - Minimum intensities in the horizontal plane of position lights.

Code of Federal Regulations, 2011 CFR

2011-01-01

...: Dihedral angle (light included) Angle from right or left of longitudinal axis, measured from dead ahead Intensity (candles) L and R (red and green) 0° to 10°10° to 20° 20° to 110° 4030 5 A (rear white) 110° to...
Crystal structure of 4-fluoro-N-[2-(4-fluorobenzoyl)hydrazine-1-carbonothioyl]benzamide

PubMed Central

Firdausiah, Syadza; Salleh Huddin, Ameera Aqeela; Hasbullah, Siti Aishah; Yamin, Bohari M.; Yusoff, Siti Fairus M.

2014-01-01

In the title compound, C15H11F2N3O2S, the dihedral angle between the fluorobenzene rings is 88.43 (10)° and that between the central semithiocarbazide grouping is 47.00 (11)°. The dihedral angle between the amide group and attached fluorobenzene ring is 50.52 (11)°; the equivalent angle between the carbonylthioamide group and its attached ring is 12.98 (10)°. The major twists in the molecule occur about the C—N—N—C bonds [torsion angle = −138.7 (2)°] and the Car—Car—C—N (ar = aromatic) bonds [−132.0 (2)°]. An intramolecular N—H⋯O hydrogen bond occurs, which generates an S(6) ring. In the crystal, the molecules are linked by N—H⋯O and N—H⋯S hydrogen bonds, generating (001) sheets. Weak C—H⋯O and C—H⋯F interactions are also observed. PMID:25309250
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.
Synthesis and studies of axial chiral bisbenzocoumarins: Aggregation-induced emission enhancement properties and aggregation-annihilation circular dichroism effects

NASA Astrophysics Data System (ADS)

Chen, Shaojin; Liu, Wei; Ge, Zhaohai; Zhang, Wenxuan; Wang, Kunpeng; Hu, Zhiqiang

2018-03-01

Axial chiral bisbenzocoumarins were synthesized for the first time by converting naphthanol units in 1,1‧-binaphthol (BINOL) molecule to the benzocoumarin rings. The substitute groups on 3,3‧-positions of bisbenzocoumarins showed significant influence on their aggregation-induced emission enhancement (AEE) properties. It was also found that BBzC1 with ester groups on 3,3‧-positions exhibit an abnormal aggregation-annihilation circular dichroism (AACD) phenomenon, which could be caused by the decrease of the dihedral angle between adjacent benzocoumarin rings in the aggregation state. The single crystal structure of BBzC1 showed that the large dihedral angle in molecule prohibited the strong π-π stacking interactions, which could be main factors for its AEE properties.
Crystal structure of 8-hydroxyquinolinium 2-carboxy-6-nitrobenzoate monohydrate

PubMed Central

Divya Bharathi, M.; Ahila, G.; Mohana, J.; Chakkaravarthi, G.; Anbalagan, G.

2015-01-01

In the title hydrated salt, C9H8NO+·C8H4NO6 −·H2O, the deprotonated carboxylate group is almost normal to its attached benzene ring [dihedral angle = 83.56 (8)°], whereas the protonated carboxylate group is close to parallel [dihedral angle = 24.56 (9)°]. In the crystal, the components are linked by N—H⋯O and O—H⋯O hydrogen bonds, generating [001] chains. The packing is consolidated by C—H⋯O and π–π [centroid-to-centroid distances = 3.6408 (9) and 3.6507 (9) Å] interactions, which result in a three-dimensional network. PMID:26029446
Flexible DNA bending in HU–DNA cocrystal structures

PubMed Central

Swinger, Kerren K.; Lemberg, Kathryn M.; Zhang, Ying; Rice, Phoebe A.

2003-01-01

HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site-specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles (∼105–140°). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU–DNA and IHF–DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU-induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU’s role as an architectural cofactor in many different systems that may require differing geometries. PMID:12853489
Vibrational spectroscopy, intramolecular CH⋯O interaction and conformational analysis of 2,5-dimethyl-benzyl benzoate

NASA Astrophysics Data System (ADS)

Viana, Rommel B.; Ribeiro, Gabriela L. O.; Valencia, Leidy J.; Varela, Jaldyr J. G.; Viana, Anderson B.; da Silva, Albérico B. F.; Moreno-Fuquen, Rodolfo

2016-12-01

The aim of this study was to report the spectroscopic and electronic properties of 2,5-dimethyl-benzyl benzoate. FT-IR and Raman vibrational spectral analyses were performed, while a computational approach was used to elucidate the vibrational frequency couplings. The electronic properties were predicted using the Density Functional Theory, while the G3MP2 method was employed in the thermochemical calculation. A conformational analysis, frontier orbitals, partial atomic charge distribution and the molecular electrostatic potential were also estimated. Concerning to the dihedral angles in the ester group, a conformational analysis showed a barrier energy of 10 kcal mol-1, while other small barriers (below 0.6 kcal mol-1) were predicted within the potential surface energy investigation. Insights into the relative stability among the different positions of methyl groups in the phenyl ring demonstrated that the energy gaps were lower than 1 kcal mol-1 among the regioisomers. In addition, the Quantum Theory of Atoms in Molecules (QTAIM) was used to understand the intramolecular CH⋯O interaction in the title compound, while various methodologies were applied in the atomic charge distribution to evaluate the susceptibility to the population method.
14 CFR 25.427 - Unsymmetrical loads.

Code of Federal Regulations, 2010 CFR

2010-01-01

... must be assumed to be subjected to unsymmetrical loading conditions determined as follows: (1) 100... tail surfaces have dihedral angles greater than plus or minus 10 degrees, or are supported by the...
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.
1-(2,4-Dinitrophenyl)-2-(1,2,3,4-tetrahydronaphthalen-1-ylidene)hydrazine

PubMed Central

Danish, M.; Hamid, Masood; Tahir, M. Nawaz; Ahmad, Nazir; Ghafoor, Sabiha

2010-01-01

In the title compound, C14H14N4O4, the dihedral angle between the benzene rings is 10.42 (8)°. The nitro groups make dihedral angles of 5.3 (2) and 6.47 (15)° with their parent ring and are oriented at 11.2 (3)° with respect to each other. An intramolecular N—H⋯O hydrogen bond completes an S(6) ring motif. In the crystal, molecules are linked by C—H⋯O interactions, thus forming (010) chains in which R 2 2(13) ring motifs are present. There also exist aromatic π–π stacking interactions [centroid–centroid separation = 3.7046 (9) Å]. PMID:21588393
5-(4-Bromophenoxy)-1-methyl-3-methyl-1H-pyrazole-4-carbaldehyde-O-[(5-methoxy-1,3,4-thiadiazol-2-yl)-methyl]oxime

PubMed Central

Fan, Chong-Guang; Chen, Jian-Cun; Dai, Hong; Wei, Yun-Hua; Shi, Yu-Jun

2012-01-01

In the title molecule, C16H16BrN5O3S, the 1,3,4-thiadiazole ring is situated under the benzene ring, forming a dihedral angle of 86.6 (2)°, and with an S⋯Cg (where Cg is the centroid of the benzene ring) distance of 3.312 (3) Å. The benzene and 1,3,4-thiadiazole rings form dihedral angles of 83.8 (3) and 57.7 (2)°, respectively, with the central pyrazole ring. In the absence of classical hydrogen bonds, the crystal packing is stabilized by a C—H⋯π interaction.. PMID:23284447

1-[5-(4-Bromophenyl)-3-(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl]butan-1-one

PubMed Central

Fun, Hoong-Kun; Loh, Wan-Sin; Sapnakumari, M.; Narayana, B.; Sarojini, B. K.

2012-01-01

In the title compound, C19H18BrFN2O, the benzene rings form dihedral angles of 5.38 (7) and 85.48 (7)° with the mean plane of the 4,5-dihydro-1H-pyrazole ring (r.m.s. deviation = 0.0849 Å), which approximates to an envelope conformation with the –CH2– group as the flap. The dihedral angle between the benzene rings is 82.86 (7)°. In the crystal, C—H⋯F and C—H⋯O hydrogen bonds link the molecules to form inversion dimers and together these generate chains along [011]. The crystal packing also features C—H⋯π interactions. PMID:22969553
Crystal structure of quinolinium 2-carboxy-6-nitro-benzoate monohydrate.

PubMed

Mohana, J; Divya Bharathi, M; Ahila, G; Chakkaravarthi, G; Anbalagan, G

2015-05-01

In the anion of the title hydrated mol-ecular salt, C9H8N(+)·C8H4NO6 (-)·H2O, the protonated carboxyl and nitro groups makes dihedral angles of 27.56 (5) and 6.86 (8)°, respectively, with the attached benzene ring, whereas the deprotonated carb-oxy group is almost orthogonal to it with a dihedral angle of 80.21 (1)°. In the crystal, the components are linked by O-H⋯O and N-H⋯O hydrogen bonds, generating [001] chains. The packing is consolidated by weak C-H⋯N and C-H⋯O inter-actions as well as aromatic π-π stacking [centroid-to-centroid distances: 3.7023 (8) & 3.6590 (9)Å] inter-actions, resulting in a three-dimensional network.
Crystal structure of N-{[3-bromo-1-(phenyl-sulfon-yl)-1H-indol-2-yl]meth-yl}benzene-sulfonamide.

PubMed

Umadevi, M; Raju, P; Yamuna, R; Mohanakrishnan, A K; Chakkaravarthi, G

2015-10-01

In the title compound, C21H17BrN2O4S2, the indole ring system subtends dihedral angles of 85.96 (13) and 9.62 (16)° with the planes of the N- and C-bonded benzene rings, respectively. The dihedral angles between the benzene rings is 88.05 (17)°. The mol-ecular conformation is stabilized by intra-molecular N-H⋯O and C-H⋯O hydrogen bonds and an aromatic π-π stacking [centroid-to-centroid distance = 3.503 (2) Å] inter-action. In the crystal, short Br⋯O [2.9888 (18) Å] contacts link the mol-ecules into [010] chains. The chains are cross-linked by weak C-H⋯π inter-actions, forming a three-dimensional network.
Benzamide-picric acid (1/1).

PubMed

Sivaramkumar, M S; Velmurugan, R; Sekar, M; Ramesh, P; Ponnuswamy, M N

2010-06-26

In the title compound, C(7)H(7)NO·C(6)H(3)N(3)O(7), one of the nitro groups of the picric acid mol-ecule lies in the plane of the attached benzene ring [dihedral angle = 1.4 (1)°] while the other two are twisted away by 9.9 (1) and 30.3 (1)°. In the benzamide mol-ecule, the amide group is almost coplanar with the benzene ring [dihedral angle = 4.4 (1)°]. An intra-molecular O-H⋯O hydrogen bond generates an S6 ring motif. In the crystal, mol-ecules are linked into a ribbon-like structure along the b axis by O-H⋯O and N-H⋯O inter-molecular hydrogen bonds. In addition, C-H⋯O hydrogen bonds and short O⋯O contacts [2.828 (2) Å] are observed.
Disequilibrium dihedral angles in dolerite sills

USGS Publications Warehouse

Holness, Marian B.; Richardson, Chris; Helz, Rosalind T.

2012-01-01

The geometry of clinopyroxene-plagioclase-plagioclase junctions in mafic rocks, measured by the median dihedral angle Θcpp, is created during solidification. In the solidifying Kilauea Iki (Hawaii) lava lake, the wider junctions between plagioclase grains are the first to be filled by pyroxene, followed by the narrower junctions. The final Θcpp, attained when all clinopyroxene-plagioclase-plagioclase junctions are formed, is 78° in the upper crust of the lake, and 85° in the lower solidification front. Θcpp in the 3.5-m-thick Traigh Bhàn na Sgùrra sill (Inner Hebrides) is everywhere 78°. In the Whin Sill (northern England, 38 m thick) and the Portal Peak sill (Antarctica, 129 m thick), Θcpp varies symmetrically, with the lowest values at the margins. The 266-m-thick Basement Sill (Antarctica) has asymmetric variation of Θcpp, attributed to a complex filling history. The chilled margins of the Basement Sill are partially texturally equilibrated, with high Θcpp. The plagioclase grain size in the two widest sills varies asymmetrically, with the coarsest rocks found in the upper third. Both Θcpp and average grain size are functions of model crystallization times. Θcpp increases from 78° to a maximum of ∼100° as the crystallization time increases from 1 to 500 yr. Because the use of grain size as a measure of crystallization time is dependent on an estimate of crystal growth rates, dihedral angles provide a more direct proxy for cooling rates in dolerites.
(E)-1-(2,4-Di-nitro-phen-yl)-2-(3-eth-oxy-4-hy-droxy-benzyl-idene)hydrazine.

PubMed

Fun, Hoong-Kun; Chantrapromma, Suchada; Ruanwas, Pumsak; Kobkeatthawin, Thawanrat; Chidan Kumar, C S

2014-01-01

The mol-ecule of the title hydrazine derivative, C15H14N4O6, is essentially planar, the dihedral angle between the substituted benzene rings being 2.25 (9)°. The eth-oxy and hy-droxy groups are almost coplanar with their bound benzene ring [r.m.s. deviation = 0.0153 (2) Å for the ten non-H atoms]. Intra-molecular N-H⋯O and O-H⋯Oeth-oxy hydrogen bonds generate S(6) and S(5) ring motifs, respectively. In the crystal, mol-ecules are linked by O-H⋯Onitro hydrogen bonds into chains propagating in [010]. Weak aromatic π-π inter-actions, with centroid-centroid distances of 3.8192 (19) and 4.0491 (19) Å, are also observed.
catena-Poly[[(benzil bis{[(pyridin-2-yl)methylidene]hydrazone}-κ⁴N,N',N'',N''')mercury(II)]-μ-chlorido-[dichloridomercury(II)]-μ-chlorido].

PubMed

Akkurt, Mehmet; Khandar, Ali Akbar; Tahir, Muhammad Nawaz; Hosseini-Yazdi, Seyed Abolfazl; Mahmoudi, Ghodrat

2012-07-01

In the title coordination polymer, [Hg₄Cl₄(C₂₆H₂₀N₆)](n), one Hg(II) ion is coordinated by four N atoms from the benzylbis((pyridin-2-yl)methyl-idenehydrazone) ligand and two Cl⁻ ions in a very distorted cis-HgCl₂N₄ octa-hedral geometry. The other Hg(II) ion is coordinated in a distorted tetra-hedral geometry by four Cl⁻ ions. Bridging chloride ions link the Hg(II) ions into a chain propagating in [010]: the Hg-Cl bridging bonds are significantly longer than the terminal bonds. The dihedral angle between the central benzene rings of the ligand is 83.3 (2)°. The packing is consolidated by weak C-H⋯Cl hydrogen bonds and C-H⋯π inter-actions.
1-(3,3-Dichloro-all-yloxy)-4-methyl-2-nitro-benzene.

PubMed

Ren, Dong-Mei

2012-06-01

In the title compound, C(10)H(9)Cl(2)NO(3), the dihedral angle between the benzene ring and the plane of the nitro group is 39.1 (1)°, while that between the benzene ring and the plane through the three C and two Cl atoms of the dichloro-all-yloxy unit is 40.1 (1)°. In the crystal, C-H⋯O hydrogen bonds to the nitro groups form chains along the b axis. These chains are linked by inversion-related pairs of Cl⋯O inter-actions at a distance of 3.060 (3) Å, forming sheets approximately parallel to [-201] and generating R(2) (2)(18) rings. π-π contacts between benzene rings in adjacent sheets, with centroid-centroid distances of 3.671 (2) Å, stack mol-ecules along c.
Comparative structural and vibrational study of the four lowest energy conformers of serotonin

NASA Astrophysics Data System (ADS)

Jha, Omkant; Yadav, T. K.; Yadav, R. A.

2017-02-01

A computational investigation of all possible lowest energy conformers of serotonin was carried out at the B3LYP/6-311 ++G** level. Out of the 14 possible lowest energy conformers, the first 4 conformers were investigated thoroughly for the optimized geometries, fundamental frequencies, the potential energy distributions, APT and natural charges, natural bond orbital (NBO) analysis, MEP, Contour map, total density array, HOMO, LUMO energies. The second third and fourth conformers are energetically at higher temperatures of 78, 94 and 312 K respectively with respect to the first one. Bond angles and bond lengths do not show significant variations while the dihedral angles vary significantly in going from one conformer to the other. Some of the vibrational modes of the indole moiety are conformation dependent to some extent whereas most of the normal modes of vibration of amino-ethyl side chain vary significantly in going from one conformer to conformer. The MEP for the four conformers suggested that the sites of the maximum positive and negative ESP change on changing the conformation. The charges at some atomic sites also change significantly from conformer to conformer.
3,3′′-Bis(9-hydroxyfluoren-9-yl)-1,1′:3′,1′′-terphenyl

PubMed Central

Skobridis, Konstantinos; Theodorou, Vassiliki; Paraskevopoulos, Georgios; Seichter, Wilhelm; Weber, Edwin

2013-01-01

The asymmetric unit of the title compound, C44H30O2, contains two independent molecules in which the terminal rings of the terphenyl element are inclined at angles of 36.3 (1) and 22.5 (1)° with respect to the central ring and the dihedral angles between the fluorenyl units are 72.3 (1) and 62.8 (1)°. In the crystal, pairs of O—H⋯O hydrogen bonds link the molecules into inversion dimers. The hydroxy H atoms not involved in these hydrogen bonds form O—H⋯π interactions in which the central terphenyl rings act as acceptors. Weak C—H⋯O contacts and π–π [centroid–centroid distance = 4.088 (2) Å] stacking interactions also occur. Taking into account directed non-covalent bonding between the molecules, the crystal is constructed of supramolecular strands extending along the a-axis direction. PMID:24098206
FT-Raman, FT-IR spectra and total energy distribution of 3-pentyl-2,6-diphenylpiperidin-4-one: DFT method.

PubMed

Subashchandrabose, S; Saleem, H; Erdogdu, Y; Rajarajan, G; Thanikachalam, V

2011-11-01

FT-Raman and FT-IR spectra were recorded for 3-pentyl-2,6-diphenylpiperidin-4-one (PDPO) sample in solid state. The equilibrium geometries, harmonic vibrational frequencies, infrared and the Raman scattering intensities were computed using DFT/6-31G(d,p) level. Results obtained at this level of theory were used for a detailed interpretation of the infrared and Raman spectra, based on the total energy distribution (TED) of the normal modes. Molecular parameters such as bond lengths, bond angles and dihedral angles were calculated and compared with X-ray diffraction data. This comparison was good agreement. The intra-molecular charge transfer was calculated by means of natural bond orbital analysis (NBO). Hyperconjugative interaction energy was more during the π-π* transition. Energy gap of the molecule was found using HOMO and LUMO calculation, hence the less band gap, which seems to be more stable. Atomic charges of the carbon, nitrogen and oxygen were calculated using same level of calculation. Copyright © 2011 Elsevier B.V. All rights reserved.
meso-4,4′-Dimethoxy-2,2′-{[(3aR,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-benzimidazole-1,3-diyl]bis(methylene)}diphenol

PubMed Central

Rivera, Augusto; Quiroga, Diego; Ríos-Motta, Jaime; Kučeraková, Monika; Dušek, Michal

2013-01-01

The title compound, C23H30N2O4, a di-Mannich base derived from 4-methoxyphenol and cis-1,2-diaminecyclohexane, has a perhydrobenzimidazolidine nucleus, in which the cyclohexane ring adopts a chair conformation and the heterocyclic ring has a half-chair conformation with a C—N—C—C torsion angles of −48.14 (15) and −14.57 (16)°. The mean plane of the heterocycle makes dihedral angles of 86.29 (6) and 78.92 (6)° with the pendant benzene rings. The molecular structure of the title compound shows the presence of two interactions between the N atoms of the imidazolidine ring and the hydroxyl groups through intramolecular O—H⋯N hydrogen bonds with graph-set motif S(6). The unobserved lone pairs of the N atoms are presumed to be disposed in a syn conformation, being only the second example of an exception to the typical ‘rabbit-ears’ effect in 1,2-diamines. PMID:24046631
(7-Chloro-2-oxo-2H-chromen-4-yl)methyl pyrrolidine-1-carbodithioate

PubMed Central

Kotresh, O.; Devarajegowda, H. C.; Shirahatti, Arunkumar; Kumar, K. Mahesh; Mahabhaleshwaraiah, N. M.

2013-01-01

In the title compound, C15H14ClNO2S2, the 2H-chromene ring system is essentially planar, with a maximum deviation of 0.0133 (10) Å. Three C atoms and their attached H atoms of the pyrrolidine ring are disordered [occupany ratio 0.874 (7):0.126 (7)] with both disorder components adopting a twisted conformation. The dihedral angle between the 2H-chromene ring system and the major occupancy component of the pyrrolidine ring is 89.45 (7)°. In the crystal, inversion dimers linked by pairs of C—H⋯S and C—H⋯O interactions generate R 2 2(24) and R 2 2(10) loops, respectively. Further C—H⋯O hydrogen bonds link the dimers into [100] chains. C—H⋯π interactions also occur and there is very weak π–π stacking [interplanar spacing = 3.650 (5) Å; centroid–centroid distance = 4.095 (7) Å] between inversion-related chlorobenzene rings. PMID:24454115
Compact representation of continuous energy surfaces for more efficient protein design

PubMed Central

Hallen, Mark A.; Gainza, Pablo; Donald, Bruce R.

2015-01-01

In macromolecular design, conformational energies are sensitive to small changes in atom coordinates, so modeling the small, continuous motions of atoms around low-energy wells confers a substantial advantage in structural accuracy; however, modeling these motions comes at the cost of a very large number of energy function calls, which form the bottleneck in the design calculation. In this work, we remove this bottleneck by consolidating all conformational energy evaluations into the precomputation of a local polynomial expansion of the energy about the “ideal” conformation for each low-energy, “rotameric” state of each residue pair. This expansion is called Energy as Polynomials in Internal Coordinates (EPIC), where the internal coordinates can be sidechain dihedrals, backrub angles, and/or any other continuous degrees of freedom of a macromolecule, and any energy function can be used without adding any asymptotic complexity to the design. We demonstrate that EPIC efficiently represents the energy surface for both molecular-mechanics and quantum-mechanical energy functions, and apply it specifically to protein design to model both sidechain and backbone degrees of freedom. PMID:26089744
Crystal structure of di-bromo-meth-oxy-seselin (DBMS), a photobiologically active pyran-ocoumarin.

PubMed

Bauri, A K; Foro, Sabine; Rahman, A F M M

2017-05-01

The title compound, C 15 H 14 Br 2 O 4 [systematic name: rac -(9 S ,10 R )-3,9-dibromo-10-methoxy-8,8-dimethyl-9,10-dihydropyrano[2,3- h ]chromen-2(8 H )-one], is a pyran-ocoumarin derivative formed by the bromination of seselin, which is a naturally occurring angular pyran-ocoumarin isolated from the Indian herb Trachyspermum stictocarpum . In the mol-ecule, the benzo-pyran ring system is essentially planar, with a maximum deviation of 0.044 (2) Å for the O atom. The di-hydro-pyran ring is in a half-chair conformation and the four essentially planar atoms of this ring form a dihedral angle of 4.6 (2)° with the benzo-pyran ring system. In the crystal, mol-ecules are linked by weak C-H⋯O hydrogen bonds, forming chains propagating along [010]. In addition, π-π stacking inter-actions, with centroid-centroid distances of 3.902 (2) and 3.908 (2) Å, link the hydrogen-bonded chains into layers parallel to (001).
Protein side chain rotational isomerization: A minimum perturbation mapping study

NASA Astrophysics Data System (ADS)

Haydock, Christopher

1993-05-01

A theory of the rotational isomerization of the indole side chain of tryptophan-47 of variant-3 scorpion neurotoxin is presented. The isomerization potential energy, entropic part of the isomerization free energy, isomer probabilities, transition state theory reaction rates, and indole order parameters are calculated from a minimum perturbation mapping over tryptophan-47 χ1×χ2 torsion space. A new method for calculating the fluorescence anisotropy from molecular dynamics simulations is proposed. The method is based on an expansion that separates transition dipole orientation from chromophore dynamics. The minimum perturbation potential energy map is inverted and applied as a bias potential for a 100 ns umbrella sampling simulation. The entropic part of the isomerization free energy as calculated by minimum perturbation mapping and umbrella sampling are in fairly close agreement. Throughout, the approximation is made that two glutamine and three tyrosine side chains neighboring tryptophan-47 are truncated at the Cβ atom. Comparison with the previous combination thermodynamic perturbation and umbrella sampling study suggests that this truncated neighbor side chain approximation leads to at least a qualitatively correct theory of tryptophan-47 rotational isomerization in the wild type variant-3 scorpion neurotoxin. Analysis of van der Waals interactions in a transition state region indicates that for the simulation of barrier crossing trajectories a linear combination of three specially defined dihedral angles will be superior to a simple side chain dihedral reaction coordinate.
(E)-N'-[1-(Thio-phen-2-yl)ethyl-idene]isonicotinohydrazide.

PubMed

Dileep, C S; Abdoh, M M M; Chakravarthy, M P; Mohana, K N; Sridhar, M A

2012-10-01

In the title compound, C(12)H(11)N(3)OS, the dihedral angle between the pyridine and thio-phene rings is 46.70 (9)° and the C-N-N-C torsion angle is 178.61 (15)°. In the crystal, inversion dimers linked by pairs of N-H⋯O hydrogen bonds generate R(2) (2)(8) loops.
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
A microstructure-based model for shape distortion during liquid phase sintering

NASA Astrophysics Data System (ADS)

Upadhyaya, Anish

Tight dimensional control is a major concern in consolidation of alloys via liquid phase sintering. This research demonstrates the role of microstructure in controlling the bulk dimensional changes that occur during liquid phase sintering. The dimensional changes were measured using a coordinate measuring machine and also on a real-time basis using in situ video imaging. To quantify compact distortion, a distortion parameter is formulated which takes into consideration the compact distortion in radial as well as axial directions. The microstructural attributes considered in this study are as follows: solid content, dihedral angle, grain size, grain contiguity and connectivity, and solid-solubility. Sintering experiments were conducted with the W-Ni-Cu, W-Ni-Fe, Mo-Ni-Cu, and Fe-Cu systems. The alloy systems and the compositions were selected to give a range of microstructures during liquid phase sintering. The results show that distortion correlates with the measured microstructural attributes. Systems containing a high solid content, high grain coordination number and contiguity, and large dihedral angle have more structural rigidity. The results show that a minimum two-dimensional grain coordination number of 3.0 is necessary for shape preservation. Based on the experimental observations, a model is derived that relates the critical solid content required for maintaining structural rigidity to the dihedral angle. The critical solid content decreases with an increasing dihedral angle. Consequently, W-Cu alloys, which have a dihedral angle of about 95sp°, can be consolidated without gross distortion with as little as 20 vol.% solid. To comprehensively understand the gravitational effects in the evolution of both the microstructure and the macrostructure during liquid phase sintering, W-Ni-Fe alloys with W content varying from 78 to 93 wt.% were sintered in microgravity. Compositions that slump during ground-based sintering also distort when sintered under microgravity. In ground-based sintering, low solid content alloys distort with a typical elephant-foot profile, while in microgravity, the compacts tend to spheroidize. This study shows that microstructural segregation occurs in both ground-based as well as microgravity sintering. In ground-based experiments, because of the density difference between the solid and the liquid phase, the solid content increases from top to the bottom of the sample. In microgravity, the solid content increases from periphery to the center of the samples. A model is derived to show that grain agglomeration and segregation are energetically favored events and will therefore be inherent to the system, even in the absence of gravity. Real time distortion measurement in alloys having appreciable solid-solubility in the liquid phase, such as W-Ni-Fe and Fe-Cu, show that the bulk of distortion occur within the first 5 min of melt formation. Distortion in such systems can be minimized by presaturating the matrix with the solid phase.
(E)-N′-(4-Methoxybenzylidene)pyridine-3-carbohydrazide dihydrate

PubMed Central

Novina, J. Josephine; Vasuki, G.; Suresh, M.; Padusha, M. Syed Ali

2013-01-01

In the title compound, C14H13N3O2·2H2O, the hydrazone molecule adopts an E conformation with respect to the C=N bond. The dihedral angle between the benzene and pyridine rings is 8.55 (10)°. The methylidene–hydrazide [–C(=O)–N–N=C–] fragment is essentially planar, with a maximum deviation of 0.0375 (13) Å. The mean planes of the benzene and pyridine rings make dihedral angles of 2.71 (14) and 11.25 (13)°, respectively, with mean plane of the methylidene-hydrazide fragment. In the crystal, the benzohydrazide and water molecules are linked by N—H⋯O, O—H⋯O and O—H⋯N hydrogen bonds into a three-dimensional network. PMID:24046719

Crystal structure of quinolinium 2-carboxy-6-nitrobenzoate monohydrate

PubMed Central

Mohana, J.; Divya Bharathi, M.; Ahila, G.; Chakkaravarthi, G.; Anbalagan, G.

2015-01-01

In the anion of the title hydrated molecular salt, C9H8N+·C8H4NO6 −·H2O, the protonated carboxyl and nitro groups makes dihedral angles of 27.56 (5) and 6.86 (8)°, respectively, with the attached benzene ring, whereas the deprotonated carboxy group is almost orthogonal to it with a dihedral angle of 80.21 (1)°. In the crystal, the components are linked by O—H⋯O and N—H⋯O hydrogen bonds, generating [001] chains. The packing is consolidated by weak C—H⋯N and C—H⋯O interactions as well as aromatic π–π stacking [centroid-to-centroid distances: 3.7023 (8) & 3.6590 (9)Å] interactions, resulting in a three-dimensional network. PMID:25995899
CACA-TOCSY with alternate 13C–12C labeling: a 13Cα direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification

PubMed Central

Takeuchi, Koh; Frueh, Dominique P.; Sun, Zhen-Yu J.; Hiller, Sebastian

2010-01-01

We present a 13C direct detection CACA-TOCSY experiment for samples with alternate 13C–12C labeling. It provides inter-residue correlations between 13Cα resonances of residue i and adjacent Cαs at positions i − 1 and i + 1. Furthermore, longer mixing times yield correlations to Cα nuclei separated by more than one residue. The experiment also provides Cα-to-sidechain correlations, some amino acid type identifications and estimates for ψ dihedral angles. The power of the experiment derives from the alternate 13C–12C labeling with [1,3-13C] glycerol or [2-13C] glycerol, which allows utilizing the small scalar 3JCC couplings that are masked by strong 1JCC couplings in uniformly 13C labeled samples. PMID:20383561
CACA-TOCSY with alternate 13C-12C labeling: a 13Calpha direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification.

PubMed

Takeuchi, Koh; Frueh, Dominique P; Sun, Zhen-Yu J; Hiller, Sebastian; Wagner, Gerhard

2010-05-01

We present a (13)C direct detection CACA-TOCSY experiment for samples with alternate (13)C-(12)C labeling. It provides inter-residue correlations between (13)C(alpha) resonances of residue i and adjacent C(alpha)s at positions i - 1 and i + 1. Furthermore, longer mixing times yield correlations to C(alpha) nuclei separated by more than one residue. The experiment also provides C(alpha)-to-sidechain correlations, some amino acid type identifications and estimates for psi dihedral angles. The power of the experiment derives from the alternate (13)C-(12)C labeling with [1,3-(13)C] glycerol or [2-(13)C] glycerol, which allows utilizing the small scalar (3)J(CC) couplings that are masked by strong (1)J(CC) couplings in uniformly (13)C labeled samples.
Crystal structure of N'-[(E)-(4-chloro-phen-yl)(phen-yl)methyl-idene]-4-methyl-benzene-sulfono-hydrazide.

PubMed

Balaji, J; Prabu, S; Xavier, J J F; Srinivasan, P

2015-01-01

The title compound, C20H17ClN2O2S, was obtained by a condensation reaction between 4-chloro-benzo-phenone and tosyl hydrazide. The plane of the methyl-substituted benzene ring forms dihedral angles of 20.12 (12) and 78.43 (13)° with those of the chlorine-substituted benzene ring and the benzene ring, respectively, with the last two rings forming a dihedral angle of 67.81 (13)°. The chlorine substituent was also found to be 0.868 (2):0.132 (2) disordered over these two rings. In the crystal, mol-ecules are linked through pairs of N-H⋯O hydrogen bonds, giving centrosymmetric cyclic dimers [graph set R 2 (2)(8)], which are linked by weak C-H⋯O and C-H⋯Cl inter-actions into a chain structure which extends along the a-axis direction.
Crystal structure of 3-benzamido-1-(4-nitro-benz-yl)quinolinium tri-fluoro-methane-sulfonate.

PubMed

Nicolas-Gomez, Mariana; Bazany-Rodríguez, Iván J; Plata-Vargas, Eduardo; Hernández-Ortega, Simón; Dorazco-González, Alejandro

2016-05-01

In the title compound, C23H18N3O3 (+)·CF3SO3 (-), the asymmetric unit contains two crystallographically independent organic cations with similar conformations. Each cation shows a moderate distortion between the planes of the amide groups and the quinolinium rings with dihedral angles of 14.90 (2) and 31.66 (2)°. The quinolinium and phenyl rings are slightly twisted with respect to each other at dihedral angles of 6.99 (4) and 8.54 (4)°. The tri-fluoro-methane-sulfonate anions are linked to the organic cations via N-H⋯O hydrogen-bonding inter-actions involving the NH amide groups. In the crystal, the organic cations are linked by weak C-H⋯O(nitro group) inter-actions into supramol-ecular chains propagating along the b-axis direction.
3-[1-(3-Hydroxybenzyl)-1H-benzimidazol-2-yl]phenol dimethyl sulfoxide monosolvate

PubMed Central

Quezada-Miriel, Magdalena; Avila-Sorrosa, Alcives; German-Acacio, Juan Manuel; Reyes-Martínez, Reyna; Morales-Morales, David

2012-01-01

Crystals of the title compound were obtained as a 1:1 dimethyl sulfoxide solvate, C20H16N2O2·C2H6O. The molecular conformation of the organic molecule is similar to that in the previously reported unsolvated structure [Eltayeb et al. (2009 ▶). Acta Cryst. E65, o1374–o1375]. Thus, the dihedral angles formed by the benzimidazole moiety with the two benzene rings are 57.54 (4) and 76.22 (5)°, and the dihedral angle between the benzene rings is 89.23 (5)°. In the crystal, a three-dimensional network features O—H⋯O, O—H⋯N and O—H⋯S hydrogen bonds, as well as C—H⋯O and C—H⋯π interactions. PMID:23125815
Benzamide–picric acid (1/1)

PubMed Central

Sivaramkumar, M. S.; Velmurugan, R.; Sekar, M.; Ramesh, P.; Ponnuswamy, M. N.

2010-01-01

In the title compound, C7H7NO·C6H3N3O7, one of the nitro groups of the picric acid molecule lies in the plane of the attached benzene ring [dihedral angle = 1.4 (1)°] while the other two are twisted away by 9.9 (1) and 30.3 (1)°. In the benzamide molecule, the amide group is almost coplanar with the benzene ring [dihedral angle = 4.4 (1)°]. An intramolecular O—H⋯O hydrogen bond generates an S6 ring motif. In the crystal, molecules are linked into a ribbon-like structure along the b axis by O—H⋯O and N—H⋯O intermolecular hydrogen bonds. In addition, C—H⋯O hydrogen bonds and short O⋯O contacts [2.828 (2) Å] are observed. PMID:21588027
Wind tunnel pressure distribution tests on a series of biplane wing models Part II : effects of changes in decalage, dihedral, sweepback and overhang

NASA Technical Reports Server (NTRS)

Knight, Montgomery; Noyes, Richard W

1929-01-01

This preliminary report furnishes information on the changes in the forces on each wing of a biplane cellule when the decalage, dihedral, sweepback and overhang are separately varied. The data were obtained from pressure distribution tests made in the Atmospheric Wind Tunnel of the Langley Memorial Aeronautical Laboratory. Since each test was carried up to 90 degree angle of attack, the results may be used in the study of stalled flight and of spinning and in the structural design of biplane wings.
Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

PubMed Central

Maadooliat, Mehdi; Huang, Jianhua Z.

2013-01-01

Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence–structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu.edu/∼madoliat/LagSVD) that can be used to produce informative animations. PMID:22926831
Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation.

PubMed

Laner, Monika; Horta, Bruno A C; Hünenberger, Philippe H

2015-02-01

The occurrence of long-timescale motions in glycerol-1-monopalmitate (GMP) lipid bilayers is investigated based on previously reported 600 ns molecular dynamics simulations of a 2×8×8 GMP bilayer patch in the temperature range 302-338 K, performed at three different hydration levels, or in the presence of the cosolutes methanol or trehalose at three different concentrations. The types of long-timescale motions considered are: (i) the possible phase transitions; (ii) the precession of the relative collective tilt-angle of the two leaflets in the gel phase; (iii) the trans-gauche isomerization of the dihedral angles within the lipid aliphatic tails; and (iv) the flipping of single lipids across the two leaflets. The results provide a picture of GMP bilayers involving a rich spectrum of events occurring on a wide range of timescales, from the 100-ps range isomerization of single dihedral angles, via the 100-ns range of tilt precession motions, to the multi-μs range of phase transitions and lipid-flipping events. Copyright © 2014 Elsevier Inc. All rights reserved.
Fast flexible modeling of RNA structure using internal coordinates.

PubMed

Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ Biagio

2011-01-01

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.
2-(3-Cyano-4-{3-[1-(2-hy-droxy-eth-yl)-3,3-dimethyl-1,3-di-hydro-indol-2-yl-idene]prop-2-en-yl}-5,5-dimethyl-5H-furan-2-yl-idene)malono-nitrile.

PubMed

Gainsford, Graeme J; Bhuiyan, M Delower H; Kay, Andrew J

2014-01-01

The title compound, C25H24N4O2, adopts a cisoid configuration and has twofold orientational disorder of the 2-hy-droxy-ethyl group. The mol-ecule is twisted from planarity so that the dihedral angle between the terminating indol-2-yl-idene and the furan-2-yl-idene moiety mean planes is 12.75 (7)°. Conformational disorder occurs at the indol-2-yl-idene N atom, which results in two orientations for the hy-droxy-ethyl group [occupancy ratio = 0.896 (2):0.104 (2)], and the hy-droxy O atom of the 2-hy-droxy-ethyl group is located over three sites [occupancy ratio = 0.548 (2):0.348 (2):0.104 (2)]. An intra-molecular C-H⋯O hydrogen bond involving the lowest occupancy hy-droxy O atom is observed. In the crystal, the mol-ecules pack in parallel dimeric sheets about centres of symmetry, utilizing O-H⋯N(cyano), C-H⋯N(cyano) and O-H⋯O hydrogen bonds, in two sets parallel to (02-1) and (021) planes.
The Packing of Helical and Zigzag Chains and Distribution of Interstitial Voids in Expanded Liquid Se near the Semiconductor to Metal Transition

NASA Astrophysics Data System (ADS)

Maruyama, Kenji; Hiroi (Sato), Satoshi; Endo, Hirohisa; Hoshino, Hideoki; Odagaki, Takashi; Hensel, Friedrich

2017-08-01

The reverse Monte Carlo (RMC) and Voronoi-Delaunay (VD) void analyses were applied to study the modification of chain geometries near the semiconductor (SC) to metal (M) transition in expanded liquid Se along the isochore of d = 3.4 g/cm3. Fluctuations of dihedral angles with increasing temperature and pressure cause modification of the helical (H) chain to the planar zigzag (Z) chain conformations. The distribution of voids size (rV ) supported by chain segments and distances to the 4th 6th neighbor atoms on the chain segments provide information on the stacking of planar zigzag chains compensated by empty space (L-voids, rV 3.6 Å) which leads to the formation of metallic domains. Near SC-M transition region the number fraction NZ/NH for Z and H chain segments increases.
(E)-1-(2,4-Dinitrophenyl)-2-(3-ethoxy-4-hydroxybenzylidene)hydrazine

PubMed Central

Fun, Hoong-Kun; Chantrapromma, Suchada; Ruanwas, Pumsak; Kobkeatthawin, Thawanrat; Chidan Kumar, C. S.

2014-01-01

The molecule of the title hydrazine derivative, C15H14N4O6, is essentially planar, the dihedral angle between the substituted benzene rings being 2.25 (9)°. The ethoxy and hydroxy groups are almost coplanar with their bound benzene ring [r.m.s. deviation = 0.0153 (2) Å for the ten non-H atoms]. Intramolecular N—H⋯O and O—H⋯Oethoxy hydrogen bonds generate S(6) and S(5) ring motifs, respectively. In the crystal, molecules are linked by O—H⋯Onitro hydrogen bonds into chains propagating in [010]. Weak aromatic π–π interactions, with centroid–centroid distances of 3.8192 (19) and 4.0491 (19) Å, are also observed. PMID:24527018
(E)-3-[3,4-Bis(meth-oxy-methoxy)phen-yl]-1-(7-hy-droxy-5-meth-oxy-2,2-dimethyl-chroman-8-yl)prop-2-en-1-one.

PubMed

Hashim, Nur Athirah; Ahmad, Farediah; Basar, Norazah; Awang, Khalijah; Ng, Seik Weng

2011-09-01

The reaction of 5,6-(2,2-dimethyl-chroman-yl)-2-hy-droxy-4-meth-oxy-acetophenone and 3,4-bis-(meth-oxy-meth-yloxy)benzaldehyde affords the intense orange title chalcone derivative, C(25)H(30)O(8). The two benzene rings are connected through a -C(=O)-CH=CH- (propenone) unit, which is in an E conformation; the ring with the hy-droxy substitutent is aligned at 19.5 (2)° with respect to this unit, whereas the ring with the meth-oxy-meth-yloxy substituent is aligned at 9.3 (3)°. The dihedral angle between the rings is 19.38 (10)°. The hy-droxy group engages in an intra-molecular O-H⋯O hydrogen bond with the carbonyl O atom of the propenone unit, generating an S(5) ring.
4-{2-[2-(4-Formylphenoxy)ethoxy]ethoxy}benzaldehyde

PubMed Central

Ma, Zhen; Cao, Yiqun

2011-01-01

The title compound, C18H18O5, was obtained by the reaction of 4-hydroxybenzaldehyde with bis(2,2-dichloroethyl) ether in dimethylformamide. In the crystal, the molecule lies on a twofold rotation axis that passes through the central O atom of the aliphatic chain, thus leading to one half-molecule being present per asymmetric unit. The carbonyl, aryl and O—CH2—CH2 groups are almost coplanar, with an r.m.s. deviation of 0.030 Å. The aromatic rings are approximately perpendicular to each other, forming a dihedral angle of 78.31 sh;H⋯O hydrogen bonds and C—H⋯π interactions help to consolidate the three-dimensional network. PMID:21754870
(E)-N′-(5-Bromo-2-hydroxybenzylidene)-2-(4-isobutylphenyl)propanohydrazide

PubMed Central

Mohamed, Shaaban K.; Horton, Peter N.; Akkurt, Mehmet; Albayati, Mustafa R.; Abdelhamid, Antar A.

2012-01-01

The title compound, C20H23BrN2O2, containing an ibuprofen core, crystallizes with three independent molecules of similar conformation in the asymmetric unit. In these three molecules, the two benzene rings make dihedral angles of 82.7 (2), 71.2 (2) and 78.0 (3)° with respect to each other. The atoms of the isobutyl groups in two of the molecules are disordered over two positions, with site-occupancy ratios of 0.516 (8):0.484 (8) and 0.580 (8):0.420 (8). In the crystal, molecules are linked by N—H⋯O, C—H⋯O and O—H⋯N hydrogen bonds. Furthermore, C—H⋯π interactions are also observed. PMID:22904830
catena-Poly[[(benzil bis{[(pyridin-2-yl)methylidene]hydrazone}-κ4 N,N′,N′′,N′′′)mercury(II)]-μ-chlorido-[dichloridomercury(II)]-μ-chlorido

PubMed Central

Akkurt, Mehmet; Khandar, Ali Akbar; Tahir, Muhammad Nawaz; Hosseini-Yazdi, Seyed Abolfazl; Mahmoudi, Ghodrat

2012-01-01

In the title coordination polymer, [Hg2Cl4(C26H20N6)]n, one HgII ion is coordinated by four N atoms from the benzylbis((pyridin-2-yl)methylidenehydrazone) ligand and two Cl− ions in a very distorted cis-HgCl2N4 octahedral geometry. The other HgII ion is coordinated in a distorted tetrahedral geometry by four Cl− ions. Bridging chloride ions link the HgII ions into a chain propagating in [010]: the Hg—Cl bridging bonds are significantly longer than the terminal bonds. The dihedral angle between the central benzene rings of the ligand is 83.3 (2)°. The packing is consolidated by weak C—H⋯Cl hydrogen bonds and C—H⋯π interactions. PMID:22807743
Crystal structure of bis-(μ-3-nitro-benzoato)-κ3O,O':O;κ3O:O,O'-bis-[bis-(3-cyano-pyridine-κN1)(3-nitro-benzoato-κ2O,O')cadmium].

PubMed

Hökelek, Tuncer; Akduran, Nurcan; Özen, Azer; Uğurlu, Güventürk; Necefoğlu, Hacali

2017-03-01

The asymmetric unit of the title compound, [Cd 2 (C 7 H 4 NO 4 ) 4 (C 6 H 4 N 2 ) 4 ], contains one Cd II atom, two 3-nitro-benzoate (NB) anions and two 3-cyano-pyridine (CPy) ligands. The two CPy ligands act as monodentate N(pyridine)-bonding ligands, while the two NB anions act as bidentate ligands through the carboxyl-ate O atoms. The centrosymmetric dinuclear complex is generated by application of inversion symmetry, whereby the Cd II atoms are bridged by the carboxyl-ate O atoms of two symmetry-related NB anions, thus completing the distorted N 2 O 5 penta-gonal-bipyramidal coordination sphere of each Cd II atom. The benzene and pyridine rings are oriented at dihedral angles of 10.02 (7) and 5.76 (9)°, respectively. In the crystal, C-H⋯N hydrogen bonds link the mol-ecules, enclosing R 2 2 (26) ring motifs, in which they are further linked via C-H⋯O hydrogen bonds, resulting in a three-dimensional network. In addition, π-π stacking inter-actions between parallel benzene rings and between parallel pyridine rings of adjacent mol-ecules [shortest centroid-to-centroid distances = 3.885 (1) and 3.712 (1) Å, respectively], as well as a weak C-H⋯π inter-action, may further stabilize the crystal structure.
14 CFR 23.1395 - Maximum intensities in overlapping beams of position lights.

Code of Federal Regulations, 2010 CFR

2010-01-01

... boundary plane at more than 10 degrees but less than 20 degrees; and (b) Area B includes all directions in the adjacent dihedral angle that pass through the light source and intersect the common boundary plane...

Crystal structures of functional building blocks derived from bis(benzo[b]thiophen-2-yl)methane.

PubMed

Katzsch, Felix; Gruber, Tobias; Weber, Edwin

2016-09-01

The syntheses of three bis(benzo[b]thiophen-2-yl)methane derivatives, namely bis(benzo[b]thiophen-2-yl)methanone, C17H10OS2, (I), 1,1-bis(benzo[b]thiophen-2-yl)-3-(trimethylsilyl)prop-2-yn-1-ol, C22H20OS2Si, (II), and 1,1-bis(benzo[b]thiophen-2-yl)prop-2-yn-1-ol, C19H12OS2, (III), are described and their crystal structures discussed comparatively. The conformation of ketone (I) and the respective analogues are rather similar for most of the compounds compared. This is true for the interplanar angles, the Caryl-Cbridge-Caryl angles and the dihedral angles. The best resemblance is found for a bioisotere of (I), viz. 2,2'-dinaphthyl ketone, (VII). By way of interest, the crystal packings also reveal similarities between (I) and (VII). In (I), the edge-to-face interactions seen between two napthyl residues in (VII) are substituted by S...π contacts between the benzo[b]thiophen-2-yl units in (I). In the structures of the bis(benzo[b]thiophen-2-yl)methanols, i.e. (II) and (III), the interplanar angles are also quite similar compared with analogues and related active pharmaceutical ingredients (APIs) containing the dithiophen-2-ylmethane scaffold, though the dihedral angles show a larger variability and produce unsymmetrical molecules.
(E)-N′-[1-(Thiophen-2-yl)ethylidene]isonicotinohydrazide

PubMed Central

Dileep, C. S.; Abdoh, M. M. M; Chakravarthy, M. P.; Mohana, K. N.; Sridhar, M. A.

2012-01-01

In the title compound, C12H11N3OS, the dihedral angle between the pyridine and thiophene rings is 46.70 (9)° and the C—N—N—C torsion angle is 178.61 (15)°. In the crystal, inversion dimers linked by pairs of N—H⋯O hydrogen bonds generate R 2 2(8) loops. PMID:23125752
Spectroscopic (FT-IR, FT-Raman, FT-NMR and UV-Vis) investigation on benzil dioxime using quantum computational methods

NASA Astrophysics Data System (ADS)

Bakkiyaraj, D.; Periandy, S.; Xavier, S.

2016-03-01

The spectral analysis of benzil dioxime is carried out using the FTIR, FT Raman, FT NMR and UV-Vis spectra of the compound with the help of quantum computations by density functional theories. The FT-IR (4000 - 400 cm-1) and FT-Raman (4000-100 cm-1) spectra are recorded in solid phase, the 1H and 13C NMR spectra in DMSO phase and the UV spectrum (200-400 nm) in ethanol phase. The different conformers of the compound and their minimum energies are studied by potential energy surface scan, using semi-empirical method PM6. The computed wavenumbers from different methods are scaled so as to agree with the experimental values and the scaling factors are reported. All the fundamental modes have been assigned based on the potential energy distribution (PED) values and the structure the molecule is analyzed interms of parameters like bond length, bond angle and dihedral angles predicted byB3LYP and CAM-B3LYP methods with cc-pVDZ basis sets. The values of dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the molecule are reported, using which the non -linear optical property of the molecule is discussed. The HOMO-LUMO mappings are reported which reveals the different charge transfer possibilities within the molecule. The isotropic chemical shifts predicted for 1H and 13C atoms using gauge invariant atomic orbital (GIAO) theory show good agreement with experimental shifts and the same is discussed in comparison with atomic charges, predicted by Mullikan and APT charge analysis. NBO analysis is carried out to picture the probable electronic transitions in the molecule.
1H-Indole-3-carbaldehyde.

PubMed

Dileep, C S; Abdoh, M M M; Chakravarthy, M P; Mohana, K N; Sridhar, M A

2012-11-01

In the title compound, C(9)H(7)NO, the benzene ring forms a dihedral angle of 3.98 (12)° with the pyrrole ring. In the crystal, N-H⋯O hydrogen bonds links the mol-ecules into chains which run parallel to [02-1].
14 CFR 27.1395 - Maximum intensities in overlapping beams of forward and rear position lights.

Code of Federal Regulations, 2010 CFR

2010-01-01

... boundary plane at more than 10 degrees but less than 20 degrees, and (b) Area B includes all directions in the adjacent dihedral angle that pass through the light source and intersect the common boundary plane...
14 CFR 25.1395 - Maximum intensities in overlapping beams of forward and rear position lights.

Code of Federal Regulations, 2010 CFR

2010-01-01

... boundary plane at more than 10 degrees but less than 20 degrees; and (b) Area B includes all directions in the adjacent dihedral angle that pass through the light source and intersect the common boundary plane...
14 CFR 29.1395 - Maximum intensities in overlapping beams of forward and rear position lights.

Code of Federal Regulations, 2010 CFR

2010-01-01

... boundary plane at more than 10 degrees but less than 20 degrees; and (b) Area B includes all directions in the adjacent dihedral angle that pass through the light source and intersect the common boundary plane...
Efficient algorithms for single-axis attitude estimation

NASA Technical Reports Server (NTRS)

Shuster, M. D.

1981-01-01

The computationally efficient algorithms determine attitude from the measurement of art lengths and dihedral angles. The dependence of these algorithms on the solution of trigonometric equations was reduced. Both single time and batch estimators are presented along with the covariance analysis of each algorithm.
Conformational differences between the methoxy groups of QA and QB site ubisemiquinones in bacterial reaction centers: a key role for methoxy group orientation in modulating ubiquinone redox potential.

PubMed

Taguchi, Alexander T; O'Malley, Patrick J; Wraight, Colin A; Dikanov, Sergei A

2013-07-09

Ubiquinone is an almost universal, membrane-associated redox mediator. Its ability to accept either one or two electrons allows it to function in critical roles in biological electron transport. The redox properties of ubiquinone in vivo are determined by its environment in the binding sites of proteins and by the dihedral angle of each methoxy group relative to the ring plane. This is an attribute unique to ubiquinone among natural quinones and could account for its widespread function with many different redox complexes. In this work, we use the photosynthetic reaction center as a model system for understanding the role of methoxy conformations in determining the redox potential of the ubiquinone/semiquinone couple. Despite the abundance of X-ray crystal structures for the reaction center, quinone site resolution has thus far been too low to provide a reliable measure of the methoxy dihedral angles of the primary and secondary quinones, QA and QB. We performed 2D ESEEM (HYSCORE) on isolated reaction centers with ubiquinones (13)C-labeled at the headgroup methyl and methoxy substituents, and have measured the (13)C isotropic and anisotropic components of the hyperfine tensors. Hyperfine couplings were compared to those derived by DFT calculations as a function of methoxy torsional angle allowing estimation of the methoxy dihedral angles for the semiquinones in the QA and QB sites. Based on this analysis, the orientation of the 2-methoxy groups are distinct in the two sites, with QB more out of plane by 20-25°. This corresponds to an ≈50 meV larger electron affinity for the QB quinone, indicating a substantial contribution to the experimental difference in redox potentials (60-75 mV) of the two quinones. The methods developed here can be readily extended to ubiquinone-binding sites in other protein complexes.
The structure of the ends of α-helices in globular proteins: effect of additional hydrogen bonds and implications for helix formation.

PubMed

Leader, David P; Milner-White, E James

2011-03-01

We prepared a set of about 2000 α-helices from a relational database of high-resolution three-dimensional structures of globular proteins, and identified additional main chain i ← i+3 hydrogen bonds at the ends of the helices (i.e., where the hydrogen bonding potential is not fulfilled by canonical i ← i+4 hydrogen bonds). About one-third of α-helices have such additional hydrogen bonds at the N-terminus, and more than half do so at the C-terminus. Although many of these additional hydrogen bonds at the C-terminus are associated with Schellman loops, the majority are not. We compared the dihedral angles at the termini of α-helices having or lacking the additional hydrogen bonds. Significant differences were found, especially at the C-terminus, where the dihedral angles at positions C2 and C1 in the absence of additional hydrogen bonds deviate substantially from those occurring within the α-helix. Using a novel approach we show how the structure of the C-terminus of the α-helix can emerge from that of constituent overlapping α-turns and β-turns, which individually show a variation in dihedral angles at different positions. We have also considered the direction of propagation of the α-helix using this approach. If one assumes that helices start as a single α-turn and grow by successive addition of further α-turns, the paths for growth in the N → C and C → N directions differ in a way that suggests that extension in the C → N direction is favored. Copyright © 2010 Wiley-Liss, Inc.
Double quantum coherence ESR spectroscopy and quantum chemical calculations on a BDPA biradical.

PubMed

Haeri, Haleh Hashemi; Spindler, Philipp; Plackmeyer, Jörn; Prisner, Thomas

2016-10-26

Carbon-centered radicals are interesting alternatives to otherwise commonly used nitroxide spin labels for dipolar spectroscopy techniques because of their narrow ESR linewidth. Herein, we present a novel BDPA biradical, where two BDPA (α,α,γ,γ-bisdiphenylene-β-phenylallyl) radicals are covalently tethered by a saturated biphenyl acetylene linker. The inter-spin distance between the two spin carrier fragments was measured using double quantum coherence (DQC) ESR methodology. The DQC experiment revealed a mean distance of only 1.8 nm between the two unpaired electron spins. This distance is shorter than the predictions based on a simple modelling of the biradical geometry with the electron spins located at the central carbon atoms. Therefore, DFT (density functional theory) calculations were performed to obtain a picture of the spin delocalization, which may give rise to a modified dipolar interaction tensor, and to find those conformations that correspond best to the experimentally observed inter-spin distance. Quantum chemical calculations showed that the attachment of the biphenyl acetylene linker at the second position of the fluorenyl ring of BDPA did not affect the spin population or geometry of the BDPA radical. Therefore, spin delocalization and geometry optimization of each BDPA moiety could be performed on the monomeric unit alone. The allylic dihedral angle θ 1 between the fluorenyl rings in the monomer subunit was determined to be 30° or 150° using quantum chemical calculations. The proton hyperfine coupling constant calculated from both energy minima was in very good agreement with literature values. Based on the optimal monomer geometries and spin density distributions, the dipolar coupling interaction between both BDPA units could be calculated for several dimer geometries. It was shown that the rotation of the BDPA units around the linker axis (θ 2 ) does not significantly influence the dipolar coupling strength when compared to the allylic dihedral angle θ 1 . A good agreement between the experimental and calculated dipolar coupling was found for θ 1 = 30°.
Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field.

PubMed

Chapman, Dail E; Steck, Jonathan K; Nerenberg, Paul S

2014-01-14

The quality of molecular dynamics (MD) simulations relies heavily on the accuracy of the underlying force field. In recent years, considerable effort has been put into developing more accurate dihedral angle potentials for MD force fields, but relatively little work has focused on the nonbonded parameters, many of which are two decades old. In this work, we assess the accuracy of protein-protein van der Waals interactions in the AMBER ff9x/ff12 force field. Across a test set of 44 neat organic liquids containing the moieties present in proteins, we find root-mean-square (RMS) errors of 1.26 kcal/mol in enthalpy of vaporization and 0.36 g/cm(3) in liquid densities. We then optimize the van der Waals radii and well depths for all of the relevant atom types using these observables, which lowers the RMS errors in enthalpy of vaporization and liquid density of our validation set to 0.59 kcal/mol (53% reduction) and 0.019 g/cm(3) (46% reduction), respectively. Limitations in our parameter optimization were evident for certain atom types, however, and we discuss the implications of these observations for future force field development.
3-(2,3-Dioxoindolin-1-yl)propanenitrile

PubMed Central

Qachchachi, Fatima-Zahrae; Kandri Rodi, Youssef; Essassi, El Mokhtar; Bodensteiner, Michael; El Ammari, Lahcen

2014-01-01

The asymmetric unit of the title compound, C11H8N2O2, contains two independent molecules (A and B). Each molecule is build up from fused five- and six-membered rings with the former linked to a cyanoethyl group. The indoline ring and two carbonyl O atoms of each molecule are nearly coplanar, with the largest deviations from the mean planes being 0.0198 (9) (molecule A) and 0.0902 (9) Å (molecule B), each by a carbonyl O atom. The fused ring system is nearly perpendicular to the mean plane passing through the cyanoethyl chains, as indicated by the dihedral angles between them of 69.72 (9) (molecule A) and 69.15 (9)° (molecule B). In the crystal, molecules are linked by C—H⋯O and π–π [intercentroid distance between inversion-related indoline (A) rings = 3.6804 (7) Å] interactions into a double layer that stacks along the a-axis direction. PMID:24765047
Experimental and theoretical studies of 3-benzyloxy-2-nitropyridine

NASA Astrophysics Data System (ADS)

Sun, Wenting; Cui, Yu; Liu, Huimin; Zhao, Haitao; Zhang, Wenqin

2012-10-01

The structure of 3-benzyloxy-2-nitropyridine has been investigated both experimentally and theoretically. The X-ray crystallography results show that the nitro group is tilted out of the pyridine ring plane by 66.4(4)°, which is mainly attributed to the electron-electron repulsions of the lone pairs in O atom of the 3-benzyloxy moiety with O atom in nitro group. An interesting centrosymmetric π-stacking molecular pair has been found in the crystalline state, which results in the approximate coplanarity of the pyridine ring with the benzene ring. The calculated results show that the dihedral angle between the nitro group and pyridine ring from the X3LYP method is much closer to the experimental data than that from the M06-2X one. The existing two conformational isomers of 3-benzyloxy-2-nitropyridine with equal energy explain well the disorder of the nitro group at room temperature. In addition, the vibrational frequencies are also calculated by the X3LYP and M06-2X methods and compared with the experimental results. The prediction from the X3LYP method coincides with the locations of the experimental frequencies well.
2,2′-(Disulfanediyl)bis[4,6-(4-fluorophenyl)pyrimidine

PubMed Central

Betz, Richard; Gerber, Thomas; Hosten, Eric; Samshuddin, Serenthimata; Narayana, Badiadka; Sarojini, Balladka K.

2012-01-01

The title compound, C32H18F4N4S2, is a disulfide symmetrically substituted with two diaza-meta-terphenyl groups. In the crystal, the molecule adopts a twisted conformation with a C—S—S—C torsion angle of −91.82 (7)°. One of the 4,6-(4-fluorophenyl)pyrimidine groups is virtually planar, with dihedral angles between the pyrimidine and benzene groups of 4.00 (8) and 5.44 (8)°, wheares the other is non-planar with analogues dihedral angles of 18.69 (8) and 26.60 (8)°. The planar 4,6-(4-fluorophenyl)pyrimidine groups are involved in π–π stacking interactions via their 4-fluorophenyl groups [centroid–centroid distances of 3.8556 (11) and 3.9284 (11) Å] that assemble the molecules into columns extended along the a axis. In addition, the structure is stabilized by C—F⋯π [F⋯centroid = 3.4017 (16) Å], C—H⋯F and C—H⋯π interactions. PMID:22347082
Structural investigation of HIV-1 nonnucleoside reverse transcriptase inhibitors: 2-Aryl-substituted benzimidazoles

NASA Astrophysics Data System (ADS)

Ziółkowska, Natasza E.; Michejda, Christopher J.; Bujacz, Grzegorz D.

2009-11-01

Acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) is one of the most destructive epidemics in history. Inhibitors of HIV enzymes are the main targets to develop drugs against that disease. Nonnucleoside reverse transcriptase inhibitors of HIV-1 (NNRTIs) are potentially effective and nontoxic. Structural studies provide information necessary to design more active compounds. The crystal structures of four NNRTI derivatives of 2-aryl-substituted N-benzyl-benzimidazole are presented here. Analysis of the geometrical parameters shows that the structures of the investigated inhibitors are rigid. The important geometrical parameter is the dihedral angle between the planes of the π-electron systems of the benzymidazole and benzyl moieties. The values of these dihedral angles are in a narrow range for all investigated inhibitors. There is no significant difference between the structure of the free inhibitor and the inhibitor in the complex with RT HIV-1. X-ray structures of the investigated inhibitors are a good basis for modeling enzyme-inhibitor interactions in rational drug design.
Stability and Control Characteristics of a Complete Airplane Model Having a Wing with Quarter-chord Line Swept Back 40 Degrees, Aspect Ratio 2.50, and Taper Ratio 0.42

NASA Technical Reports Server (NTRS)

Schulderfrei, Marvin; Comisarow, Paul; Goodson, Kenneth W

1951-01-01

An investigation has been made of a complete airplane model having a wing with the quarter-chord line swept back 40 degrees, aspect ratio 2.50, and taper ratio 0.42 to determine its low-speed stability and control characteristics. The longitudinal stability investigation included stabilizer and tail-off tests with different wing dihedral angles (Gamma = 0 degrees and Gamma = -10 degrees) over an angle-of-attack range for the cruising and landing configurations and tests. with a high horizontal-tail location (Gamma = -10 degrees) for the cruising configuration. Tests were made of the wing alone and to determine the effect of wing end plates in pitch. Lateral stability characteristics were determined for the airplane with different geometric wing dihedrals, with end plates, and with several dorsal modifications. Tests were made with ailerons and spoilers to determine control characteristics.
Molecular Dynamics Simulations of Hydrophobic Residues

NASA Astrophysics Data System (ADS)

Caballero, Diego; Zhou, Alice; Regan, Lynne; O'Hern, Corey

2013-03-01

Molecular recognition and protein-protein interactions are involved in important biological processes. However, despite recent improvements in computational methods for protein design, we still lack a predictive understanding of protein structure and interactions. To begin to address these shortcomings, we performed molecular dynamics simulations of hydrophobic residues modeled as hard spheres with stereo-chemical constraints initially at high temperature, and then quenched to low temperature to obtain local energy minima. We find that there is a range of quench rates over which the probabilities of side-chain dihedral angles for hydrophobic residues match the probabilities obtained for known protein structures. In addition, we predict the side-chain dihedral angle propensities in the core region of the proteins T4, ROP, and several mutants. These studies serve as a first step in developing the ability to quantitatively rank the energies of designed protein constructs. The success of these studies suggests that only hard-sphere dynamics with geometrical constraints are needed for accurate protein structure prediction in hydrophobic cavities and binding interfaces. NSF Grant PHY-1019147
N-(2-{[5-Bromo-2-(morpholin-4-yl)pyrimidin-4-yl]sulfanyl}-4-methoxyphenyl)-4-chlorobenzenesulfonamide

PubMed Central

Kumar, Mohan; Mallesha, L.; Sridhar, M. A.; Kapoor, Kamini; Gupta, Vivek K.; Kant, Rajni

2012-01-01

In the title compound, C21H20BrClN4O4S2, the benzene rings bridged by the sulfonamide group are tilted relative to each other by a dihedral angle of 70.2 (1)° and the dihedral angle between the sulfur-bridged pyrimidine and benzene rings is 69.5 (1)°. The molecular conformation is stabilized by a weak intramolecular π–π stacking interaction between the pyrimidine and the 4-chlorobenzene rings [centroid–centroid distance = 3.978 (2) Å]. The morpholine ring adopts a chair conformation. In the crystal, molecules are linked into inversion dimers by pairs of C—H⋯N hydrogen bonds and these dimers are further connected by N—H⋯O hydrogen bonds, forming a tape along the a axis. PMID:22969673
(1E,4E)-1,5-Bis[4-(diethylamino)phenyl]penta-1,4-dien-3-one

PubMed Central

Ruanwas, Pumsak; Chantrapromma, Suchada; Ghabbour, Hazem A.; Fun, Hoong-Kun

2014-01-01

There are two crystallograpically independent molecules in the asymmetric unit of the title bischalcone derivative, C25H32N2O. Both molecules are twisted with a dihedral angle between the two substituted benzene rings of 11.19 (16)° in one molecule and 14.40 (15)° in the other. The central penta-1,4-dien-3-one fragments make dihedral angles of 8.49 (17) and 4.26 (17)° with the two adjacent benzene rings in one molecule, whereas the corresponding values are 8.42 (16) and 6.18 (16)° in the other. In the crystal, molecules are arranged into chains along the c-axis direction. Adjacent chains are inter-linked by weak intermolecular C—H⋯O interactions. The crystal is further stabilized by C—H⋯π interactions. PMID:24860388

(E)-4-Methoxy-N′-[(6-methyl-4-oxo-4H-chromen-3-yl)methylidene]benzohydrazide monohydrate

PubMed Central

Ishikawa, Yoshinobu; Watanabe, Kohzoh

2014-01-01

In the title hydrate, C19H16N2O4·H2O, the 4H-chromen-4-one segment is slightly twisted, with a dihedral angle between the two six-membered rings of 3.30 (5)°. The dihedral angles between the plane of the pyranone ring and the hydrazide plane and between the planes of the pyranone ring and the benzene ring of the p-methoxybenzene unit are 26.69 (4) and 2.23 (3)°, respectively. The molecule is connected to the solvent water molecule by an N—H⋯O hydrogen bond. In the crystal, there are π–π stacking interactions between centrosymmetrically related pyranone rings [centroid–centroid distance = 3.5394 (9) Å], as well as bridges formed by the water molecules via O—H⋯O hydrogen bonds. PMID:25161570
DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez, Mark A.; Sava Gallis, Dorina F.; Chavez, James S.

We report here the synthesis of a neutral viologen derivative, C 24H 16N 2O 4·2H 2O. The non-solvent portion of the structure (Z-Lig) is a zwitterion, consisting of two positively charged pyridinium cations and two negatively charged carboxylate anions. The carboxylate group is almost coplanar [dihedral angle = 2.04 (11)°] with the benzene ring, whereas the dihedral angle between pyridine and benzene rings is 46.28 (5)°. TheZ-Lig molecule is positioned on a center of inversion (Fig. 1). The presence of the twofold axis perpendicular to thec-glide plane in space groupC2/c generates a screw-axis parallel to thebaxis that is shifted from themore » origin by 1/4 in theaandcdirections. This screw-axis replicates the molecule (and solvent water molecules) through space. TheZ-Lig molecule links to adjacent moleculesviaO—H...O hydrogen bonds involving solvent water molecules as well as intermolecular C—H...O interactions. There are also π–π interactions between benzene rings on adjacent molecules.« less
Crystal structure of 3-benzamido-1-(4-nitrobenzyl)quinolinium trifluoromethanesulfonate

PubMed Central

Nicolas-Gomez, Mariana; Bazany-Rodríguez, Iván J.; Plata-Vargas, Eduardo; Hernández-Ortega, Simón; Dorazco-González, Alejandro

2016-01-01

In the title compound, C23H18N3O3 +·CF3SO3 −, the asymmetric unit contains two crystallographically independent organic cations with similar conformations. Each cation shows a moderate distortion between the planes of the amide groups and the quinolinium rings with dihedral angles of 14.90 (2) and 31.66 (2)°. The quinolinium and phenyl rings are slightly twisted with respect to each other at dihedral angles of 6.99 (4) and 8.54 (4)°. The trifluoromethanesulfonate anions are linked to the organic cations via N—H⋯O hydrogen-bonding interactions involving the NH amide groups. In the crystal, the organic cations are linked by weak C—H⋯O(nitro group) interactions into supramolecular chains propagating along the b-axis direction. PMID:27308033
Spatio-temporal coordination among functional residues in protein

NASA Astrophysics Data System (ADS)

Dutta, Sutapa; Ghosh, Mahua; Chakrabarti, J.

2017-01-01

The microscopic basis of communication among the functional sites in bio-macromolecules is a fundamental challenge in uncovering their functions. We study the communication through temporal cross-correlation among the binding sites. We illustrate via Molecular Dynamics simulations the properties of the temporal cross-correlation between the dihedrals of a small protein, ubiquitin which participates in protein degradation in eukaryotes. We show that the dihedral angles of the residues possess non-trivial temporal cross-correlations with asymmetry with respect to exchange of the dihedrals, having peaks at low frequencies with time scales in nano-seconds and an algebraic tail with a universal exponent for large frequencies. We show the existence of path for temporally correlated degrees of freedom among the functional residues. We explain the qualitative features of the cross-correlations through a general mathematical model. The generality of our analysis suggests that temporal cross-correlation functions may provide convenient theoretical framework to understand bio-molecular functions on microscopic basis.
Dynamics and control of robotic aircraft with articulated wings

NASA Astrophysics Data System (ADS)

Paranjape, Aditya Avinash

There is a considerable interest in developing robotic aircraft, inspired by birds, for a variety of missions covering reconnaissance and surveillance. Flapping wing aircraft concepts have been put forth in light of the efficiency of flapping flight at small scales. These aircraft are naturally equipped with the ability to rotate their wings about the root, a form of wing articulation. This thesis covers some problems concerning the performance, stability and control of robotic aircraft with articulated wings in gliding flight. Specifically, we are interested in aircraft without a vertical tail, which would then use wing articulation for longitudinal as well as lateral-directional control. Although the dynamics and control of articulated wing aircraft share several common features with conventional fixed wing aircraft, the presence of wing articulation presents several unique benefits as well as limitations from the perspective of performance and control. One of the objective of this thesis is to understand these features using a combination of theoretical and numerical tools. The aircraft concept envisioned in this thesis uses the wing dihedral angles for longitudinal and lateral-directional control. Aircraft with flexible articulated wings are also investigated. We derive a complete nonlinear model of the flight dynamics incorporating dynamic CG location and the changing moment of inertia. We show that symmetric dihedral configuration, along with a conventional horizontal tail, can be used to control flight speed and flight path angle independently of each other. This characteristic is very useful for initiating an efficient perching maneuver. It is shown that wing dihedral angles alone can effectively regulate sideslip during rapid turns and generate a wide range of equilibrium turn rates while maintaining a constant flight speed and regulating sideslip. We compute the turning performance limitations that arise due to the use of wing dihedral for yaw control, and compare the steady state performance of rigid and flexible-winged aircraft. We present an intuitive but very useful notion, called the effective dihedral, which allows us to extend some of the stability and performance results derived for rigid aircraft to flexible aircraft. In the process, we identify the extent of flexibility needed to induce substantial performance benefits, and conversely the extent to which results derived for rigid aircraft apply to a flexible aircraft. We demonstrate, interestingly enough, that wing flexibility actually causes a deterioration in the maximum achievable turn rate when the sideslip is regulated. We also present experimental results which help demonstrate the capability of wing dihedral for control and for executing maneuvers such as slow, rapid descent and perching. Open loop as well as closed loop experiments are performed to demonstrate (a) the effectiveness of symmetric dihedral for flight path angle control, (b) yaw control using asymmetric dihedral, and (c) the elements of perching. Using a simple order of magnitude analysis, we derive conditions under which the wing is structurally statically stable, as well as conditions under which there exists time scale separation between the bending and twisting dynamics. We show that the time scale separation depends on the geometry of the wing cross section, the Poisson's ratio of the wing material, the flight speed and the aspect ratio of the wing. We design independent control laws for bending and twisting. A key contribution of this thesis is the formulation of a partial differential equation (PDE) boundary control problem for wing deformation. PDE-backstepping is used to derive tracking and exponentially stabilizing boundary control laws for wing twist which ensure that a weighted integral of the wing twist (net lift or the rolling moment) tracks the desired time-varying reference input. We show that a control law which only ensures tracking of a weighted integral improves the stability margin of the twisting dynamics sixteen fold. A tracking control law is derived for the wing tip displacement which uses motion planning and a novel two-stage perturbation observer. This work on PDE-based control of wing deformation allows for the use of highly flexible wings on MAVs. Put together, the thesis provides a comprehensive understanding of the flight dynamics of a robotic aircraft equipped with articulated wings, and provides a set of control laws for performing agile maneuvers and for honing the benefits of using highly flexible wings.
Crystal structure of tetra-aqua-bis(3,5-di-amino-4H-1,2,4-triazol-1-ium)cobalt(II) bis-[bis-(pyridine-2,6-di-carboxyl-ato)cobaltate(II)] dihydrate.

PubMed

Johnson, Atim; Mbonu, Justina; Hussain, Zahid; Loh, Wan-Sin; Fun, Hoong-Kun

2015-06-01

The asymmetric unit of the title compound, [Co(C2H6N5)2(H2O)4][Co(C7H3NO4)2]2·2H2O, features 1.5 Co(II) ions (one anionic complex and one half cationic complex) and one water mol-ecule. In the cationic complex, the Co(II) atom is located on an inversion centre and is coordinated by two triazolium cations and four water mol-ecules, adopting an octa-hedral geometry where the N atoms of the two triazolium cations occupy the axial positions and the O atoms of the four water mol-ecules the equatorial positions. The two triazole ligands are parallel offset (with a distance of 1.38 Å between their planes). In the anionic complex, the Co(II) ion is six-coordinated by two N and four O atoms of the two pyridine-2,6-di-carboxyl-ate anions, exhibiting a slightly distorted octa-hedral coordination geometry in which the mean plane of the two pyridine-2,6-di-carboxyl-ate anions are almost perpendicular to each other, making a dihedral angle of 85.87 (2)°. In the crystal, mol-ecules are linked into a three-dimensional network via C-H⋯O, C-H⋯N, O-H⋯O and N-H⋯O hydrogen bonds.
Dipotassium tetrakis(thiocyanato-κS)palladate(II)–(2,2′-bipyrimidine-κ2 N 1,N 1′)bis(thiocyanato-κS)palladium(II) (1/2)

PubMed Central

Ha, Kwang

2012-01-01

The asymmetric unit of the title compound, K2[Pd(NCS)4]·2[Pd(NCS)2(C8H6N4)], contains two crystallographically independent half-molecules of the anionic PdII complex, two K+ cations and two independent neutral PdII complexes; an inversion centre is located at the centroid of each anionic complex. In the anionic complexes, each PdII ion is four-coordinated in an almost regular square-planar environment by four S atoms from four SCN− anions, and the PdS4 unit is exactly planar. In the neutral complexes, the PdII ion has a slightly distorted square-planar coordination environment defined by two pyrimidine N atoms derived from a chelating 2,2′-bipyrimidine ligand and two mutually cis S atoms from two SCN− anions. Both 2,2′-bipyrimidine ligands are almost planar [dihedral angle between the rings = 3.98 (16) and 4.57 (17)°] and also chelate to a potassium ion from their other two N atoms. In the crystal, the K+ ions interact with various S and N atoms of the ligands, forming a three-dimensional polymeric network, in which the shortest K⋯K contacts between the KN7S polyhedra are 4.4389 (17) and 4.4966 (18) Å. Intra- and intermolecular C—H⋯S and C—H⋯N hydrogen bonds are also observed. PMID:22590117
1H-Indole-3-carbaldehyde

PubMed Central

Dileep, C. S.; Abdoh, M. M. M.; Chakravarthy, M. P.; Mohana, K. N.; Sridhar, M. A.

2012-01-01

In the title compound, C9H7NO, the benzene ring forms a dihedral angle of 3.98 (12)° with the pyrrole ring. In the crystal, N–H⋯O hydrogen bonds links the molecules into chains which run parallel to [02-1]. PMID:23284457
Kaleidoscopes and Mathematics: An Elegant Connection

ERIC Educational Resources Information Center

Miller, Catherine M.

2017-01-01

This article describes a project in which students investigate the question: What dihedral angles between pairs of mirrors in a kaleidoscope result in perfectly symmetric images? The unit culminates with students building their own kaleidoscopes. This content aligns with parts of the Common Core's standards for fifth grade (classify…
2-[(4-Chlorophenyl)selanyl]-3,4-dihydro-2H-benzo[h]chromene-5,6-dione: crystal structure and Hirshfeld analysis

PubMed Central

Prado, Karinne E.; Name, Luccas L.; Jotani, Mukesh M.

2017-01-01

The title organoselenium compound, C19H13ClO3Se {systematic name: 2-[(4-chlorophenyl)selanyl]-2H,3H,4H,5H,6H-naphtho[1,2-b]pyran-5,6-dione}, has the substituted 2-pyranyl ring in a half-chair conformation with the methylene-C atom bound to the methine-C atom being the flap atom. The dihedral angle between the two aromatic regions of the molecule is 9.96 (9)° and indicates a step-like conformation. An intramolecular Se⋯O interaction of 2.8122 (13) Å is noted. In the crystal, π–π contacts between naphthyl rings [inter-centroid distance = 3.7213 (12) Å] and between naphthyl and chlorobenzene rings [inter-centroid distance = 3.7715 (13) Å], along with C—Cl⋯π(chlorobenzene) contacts, lead to supramolecular layers parallel to the ab plane, which are connected into a three-dimensional architecture via methylene-C—H⋯O(carbonyl) interactions. The contributions of these and other weak contacts to the Hirshfeld surface is described. PMID:28638659
1,5-Bis(1-phenyl-ethyl-idene)thio-carbono-hydrazide.

PubMed

Feng, Lei; Ji, Haiwei; Wang, Renliang; Ge, Haiyan; Li, Li

2011-06-01

The title mol-ecule, C(17)H(18)N(4)S, is not planar, as indicated by the dihedral angle of 27.24 (9)° between the two benzene rings. In the crystal, inter-molecular N-H⋯S hydrogen bonds link pairs of mol-ecules into inversion dimers.
PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

PubMed

Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

2008-11-01

The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/.
Pickett angles and Cremer-Pople coordinates as collective variables for the enhanced sampling of six-membered ring conformations

NASA Astrophysics Data System (ADS)

Sega, M.; Autieri, E.; Pederiva, F.

2011-01-01

Although completely equivalent for the description of puckered ring conformers, the two popular coordinates sets of Strauss-Pickett dihedral angles and Cremer-Pople spherical coordinates are shown to have contrasting features when employed as collective variables in free-energy calculations with accelerated sampling techniques. Results from a 100 ns molecular dynamics simulation at conformational equilibrium and from combined metadynamics/umbrella sampling calculations of glucose are exploited to elucidate these differences.
1-Allyl-3-chloro-5-nitro-1H-indazole

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Spinelli, Domenico; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

In the title compound, C10H8ClN3O2, the indazole ring system makes a dihedral angle of 7.9 (3)° with the plane through the nitro group. The allyl group is rotated out of the plane of the indazole ring system [N—N—C—C torsion angle = 104.28 (19)°]. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming zigzag chains propagating along the b-axis direction. PMID:24427047
1-Allyl-3-chloro-5-nitro-1H-indazole.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Spinelli, Domenico; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

In the title compound, C10H8ClN3O2, the indazole ring system makes a dihedral angle of 7.9 (3)° with the plane through the nitro group. The allyl group is rotated out of the plane of the indazole ring system [N-N-C-C torsion angle = 104.28 (19)°]. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming zigzag chains propagating along the b-axis direction.
Influence of the pH value of a colloidal gold solution on the absorption spectra of an LSPR-assisted sensor

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

Zhu, Jin; Li, Wenbin; Zhu, Mao

2014-03-15

The localized surface plasmon resonances (LSPRs) of gold particles assembled on a crystal plate are a powerful tool for biological sensors. Here, we prepare gold colloids in different pH solutions. We monitor the effects of the particle radius and particle coverage on the absorption spectra of AT-cut (r-face dihedral angle of about 3°) crystal plates supporting gold nanoparticles. The surface morphologies were monitored on silicon dioxide substrates using ultraviolet and visible (UV-vis) spectroscopy, and atomic force microscopy (AFM). The results showed that the gold particle coverage decreases with increasing pH value of the gold colloid solution. This phenomenon demonstrates thatmore » self-assembled gold surfaces were formed via the electrostatic adsorption of gold particles on the positively charged, ionized amino groups on the crystal plates in the acidic solution. The spectrum of gold nanoparticles with different coverage degree on the crystal plates showed that the LSPR properties are highly dependent on pH.« less
Simultaneous gauche and anomeric effects in α-substituted sulfoxides.

PubMed

Freitas, Matheus P

2012-09-07

α-Substituted sulfoxides can experience both gauche and anomeric effects, since these compounds have the geometric requirements and strong electron donor and acceptor orbitals which are essential to make operative the hyperconjugative nature of these effects. Indeed, the title effects were calculated to take place for 1,3-oxathiane 3-oxide in polar solution, where dipolar effects are absent or at least minimized, while only the gauche effect is present in 2-fluorothiane 1-oxide. Since the fluorine atom is a suitable probe for structural analysis using NMR, the (1)J(CF) dependence on the rotation around the F-C-S═O dihedral angle of (fluoromethyl)methyl sulfoxide was evaluated; differently from 1,2-difluoroethane and fluoro(methoxy)methane, this coupling constant is at least not exclusively dependent on dipolar interactions (or on hyperconjugation). Because of the nonmonotonic behavior of the (1)J(CF) rotational profile, this coupling constant does not appear to be of significant diagnostic value for probing the conformations of α-fluoro sulfoxides.
Side-chain mobility in the folded state of Myoglobin

NASA Astrophysics Data System (ADS)

Lammert, Heiko; Onuchic, Jose

We study the accessibility of alternative side-chain rotamer configurations in the native state of Myoglobin, using an all-atom structure-based model. From long, unbiased simulation trajectories we determine occupancies of rotameric states and also estimate configurational and vibrational entropies. Direct sampling of the full native-state dynamics, enabled by the simple model, reveals facilitation of side-chain motions by backbone dynamics. Correlations between different dihedral angles are quantified and prove to be weak. We confirm global trends in the mobilities of side-chains, following burial and also the chemical character of residues. Surface residues loose little configurational entropy upon folding; side-chains contribute significantly to the entropy of the folded state. Mobilities of buried side-chains vary strongly with temperature. At ambient temperature, individual side-chains in the core of the protein gain substantial access to alternative rotamers, with occupancies that are likely observable experimentally. Finally, the dynamics of buried side-chains may be linked to the internal pockets, available to ligand gas molecules in Myoglobin.
Diaquabis{5-carboxy-2-[(1H-1,2,4-triazol-1-yl)methyl]-1H-imidazole-4-carboxylato}manganese(II)

PubMed Central

Ding, De-Gang; Tong, Yan

2010-01-01

In the title compound, [Mn(C8H6N5O4)2(H2O)2], the MnII ion is situated on an inversion center and is six-coordinated by two N and two O atoms from two L ligands (HL = 2-[(1H-1,2,4-triazol-1-yl)methyl]-1H-imidazole-4,5-dicarboxylic acid) and two water molecules in a distorted octahedral geometry. In ligand L, the imidazole and triazole rings form a dihedral angle of 74.25 (8)°. Molecules are assembled into a three-dimensional structure via intermolecular O—H⋯O, O—H⋯N and N—H⋯N hydrogen-bonds, and π–π interactions with a short distance of 3.665 (2) Å between the centroids of the imidazole and triazole rings of neighbouring molecules. PMID:21579014
Research on the differences between 2-(2-Chlorophenyl)benzimidazole and 2-(4-Chlorophenyl)benzimidazole based on terahertz time domain spectroscopy

NASA Astrophysics Data System (ADS)

Song, Maojiang; Yang, Fei; Liu, Liping; Shen, Li; Hu, Pengfei; Zhang, Li; Su, Caixia

2018-05-01

Due to wide variety of biological and pharmacological activities of benzimidazole derivatives, the differences between 2-(2-Chlorophenyl)benzimidazole and 2-(4-Chlorophenyl) benzimidazole were researched by employing terahertz time-domain spectroscopy and density functional theory systematically. Although the only difference between their molecular configurations is the arrangement of chlorine atom on chlorophenyl ring, there are distinctive differences in their fingerprint spectra in the range of 0.2-2.5 THz, such as amount, amplitude, and frequency position of absorption peaks. The validity of these results was confirmed by the theoretical results simulated by using density functional theory. The possible reasons of these differences originate from the different van der Waals forces and the different dihedral angles of the molecules within crystal cell. These results indicate the importance of this spectral range as a conformational fingerprint region where even minor changes in the molecular configuration lead to major differences in its THz absorption.

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

PubMed

Cossio, Pilar; Laio, Alessandro; Pietrucci, Fabio

2011-06-14

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are different. By analyzing microseconds-long all-atom molecular dynamics simulations of a polypeptide, we find that a distance based on backbone dihedral angles performs very well in distinguishing structures that are kinetically correlated from those that are not, while the widely used C(α) root mean square distance performs more poorly. The root mean square difference between contact matrices turns out instead to be the metric providing the highest clustering coefficient, namely, according to this similarity measure, the neighbors of a structure are also, on average, neighbors among themselves. We also propose a combined distance measure which, for the system considered here, performs well both for distinguishing structures which are distant in time and for giving a consistent cluster analysis. This journal is © the Owner Societies 2011
(2E)-3-(6-Methoxynaphthalen-2-yl)-1-[4-(methylsulfanyl)phenyl]prop-2-en-1-one

PubMed Central

Fun, Hoong-Kun; Chia, Tze Shyang; Padaki, Mahesh; Isloor, Arun M.; Ismail, A. F.

2012-01-01

The asymmetric unit of the title compound, C21H18O2S, consists of two crystallographically independent molecules (A and B). The molecules exist in a trans conformation with respect to the central C=C bond. The naphthalene ring system makes dihedral angles of 51.62 (12) (molecule A) and 52.69 (12)° (molecule B) with the benzene ring. In molecule A, the prop-2-en-1-one group forms dihedral angles of 22.84 (15) and 29.02 (12)° with the adjacent naphthalene ring system and benzene ring, respectively, whereas the corresponding angles are 30.04 (12) and 23.33 (12)° in molecule B. In the crystal, molecules are linked by intermolecular C—H⋯O hydrogen bonds into head-to-tail chains along the a axis. The crystal packing also features C—H⋯π interactions. The crystal studied was a pseudo-merohedral twin with twin law (100 0-10 00-1) and a refined component ratio of 0.6103 (16):0.3897 (16). PMID:22798922
Lateral Stability and Control Measurements of a 0.0858-Scale Model of the Lockheed XF-104 Airplane at Transonic Speeds

NASA Technical Reports Server (NTRS)

Arabian, Donald D.; Schmeer, James W.

1955-01-01

An investigation of the lateral stability and control effectiveness of a 0.0858-scale model of the Lockheed XF-104 airplane has been conducted in the Langley 16-foot transonic tunnel. The model has a low aspect ratio, 3.4-percent-thick wing with negative dihedral. The horizontal tail is located on top of the vertical tail. The investigation was made through a Mach number range of 0.80 to 1.06 at sideslip angles of -5 deg. to 5 deg. and angles of attack from 0 deg. to 16 deg. The control effectiveness of the aileron, rudder, and yaw damper were determined through the Mach number and angle-of-attack range. The results of the investigation indicated that the directional stability derivative was stable and that positive effective dihedral existed throughout the lift-coefficient range and Mach number range tested. The total aileron effectiveness, which in general produced favorable yaw with rolling moment, remained fairly constant for lift coefficients up to about 0.8 for the Mach number range tested. Yawing-moment effectiveness of the rudder changed little through the Mach number range. However, the yaw damper effectiveness decreased about 30 percent at the intermediate test Mach numbers.
N-(1,3-Thiazol-2-yl)benzamide

PubMed Central

Zonouzi, Afsaneh; Mirzazadeh, Roghieh; Rahmani, Hossein; Ng, Seik Weng

2009-01-01

The title compound, C10H8N2OS, features a nonplanar molecule [dihedral angle between the two aromatic rings = 43.6 (1)°]. Two molecules are linked by N—H⋯N hydrogen bonds about a centre of inversion, giving rise to a hydrogen-bonded dimer. PMID:21582538
3-Benzylsulfanyl-1H-1,2,4-triazol-5-amine

PubMed Central

Zhang, Shuai; Liu, Pei-Jiang; Ma, Dong-Sheng; Hou, Guang-Feng

2012-01-01

In the title molecule, C9H10N4S, the dihedral angle between the benzene and triazole rings is 81.05 (5)°. In the crystal, N—H⋯N hydrogen bonds link the molecules into infinite zigzag chains along [010]. PMID:22259582
27ps DFTMD Simulations of Maltose using a Reduced Basis Set

USDA-ARS?s Scientific Manuscript database

The disaccharide, a-maltose, has been studied using constant energy density functional molecular dynamics (DFTMD) at the B3LYP/6-31+G*/4-31G+COSMO (solvent) level of theory. Maltose is of particular interest as the variation in glycosidic dihedral angles has been found to be dependent upon the star...
(E)-N-[(6-Bromopyridin-2-yl)methylidene]-4-methylaniline

PubMed Central

Cai, Mingjian; Ma, Penggao; Wang, Xiuge; Sun, Tao

2011-01-01

The title compound, C13H11BrN2, a Schiff base obtained from 6-bromopicolinaldehyde and p-toluidine, has an E configuration about the C=N bond. The dihedral angle between the benzene and pyridine rings is 30.4 (1)°. PMID:22058956
1-(4-Chlorobenzylideneamino)pyridinum iodide

PubMed Central

Cui, Yong-Tao; Wang, Jian-Qiang; Ji, Chun-Xiang; Wang, Hai-Bo; Cheng, Guo

2009-01-01

In the title compound, C12H10ClN2 +·I−, the aromatic rings are oriented at a dihedral angle of 54.55 (3)°. In the crystal structure, intermolecular C—H⋯I and C—H⋯Cl hydrogen bonds link the molecules. PMID:21581845
4-[(3-Chloro-2-methyl-phen-yl)imino-meth-yl]phenol.

PubMed

Manjunath, B C; Abdoh, M M M; Mallesha, L; Mohana, K N; Lokanath, N K

2012-11-01

In the title compound, C(14)H(12)ClNO, the dihedral angle between the aromatic rings is 39.84 (7)°. In th crystal, mol-ecules are connected by O-H⋯N hydrogen bonds into chains parallel to [001]. In addition, a C-H⋯π contact occurs.
1-(3,3-Dichloro-all-yloxy)-2-nitro-benzene.

PubMed

Ren, Dong-Mei; Wang, Yong-Yi

2012-04-01

In the title compound, C(9)H(7)Cl(2)NO(3), the dihedral angle between the benzene ring and the plane of the nitro group is 50.2 (1)°, and that between the benzene ring and the best plane through the dichloro-allyl fragment is 40.1 (1)°.
14 CFR 23.1389 - Position light distribution and intensities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... overlapping beams, within dihedral angles L, R, and A, and must meet the following requirements: (1... clarity. When the peak intensity of the left and right position lights is more than 100 candles, the... the right and left of the axis of maximum illumination. [Doc. No. 4080, 29 FR 17955, Dec. 18, 1964, as...
Methyl (2Z)-2-bromomethyl-3-(3-chlorophenyl)prop-2-enoate

PubMed Central

Swaminathan, K.; Sethusankar, K.; Selvakumar, Raman; Bakthadoss, Manickam

2013-01-01

There are two independent molecules (A and B) in the asymmetric unit of the title compound C11H10BrClO2, which represents the Z isomer. The methylacrylate moieties are essentially planar, within 0.084 (2) and 0.027 (5) Å in molecules A and B, respectively. The benzene ring makes dihedral angles of 13.17 (7) and 27.89 (9)° with the methylacrylate moiety in molecules A and B, respectively. The methylbromide moiety is almost orthogonal to the benzene ring, making dihedral angles of 81.46 (16)° in molecule A and 79.61 (16)° in molecule B. The methylacrylate moiety exhibits an extended trans conformation in both molecules. In the crystal, pairs of C—H⋯O hydrogen bonds result in the formation of quasi-centrosymmetric R 2 2(14) AB dimers. PMID:23795037
On the Angular Dependence of the Vicinal Fluorine-Fluorine Coupling Constant in 1,2-Difluoroethane: Deviation from a Karplus-like Shape.

PubMed

Provasi, Patricio F; Sauer, Stephan P A

2006-07-01

The angular dependence of the vicinal fluorine-fluorine coupling constant, (3)JFF, for 1,2-difluoroethane has been investigated with several polarization propagator methods. (3)JFF and its four Ramsey contributions were calculated using the random phase approximation (RPA), its multiconfigurational generalization, and both second-order polarization propagator approximations (SOPPA and SOPPA(CCSD)), using locally dense basis sets. The geometries were optimized for each dihedral angle at the level of density functional theory using the B3LYP functional and fourth-order Møller-Plesset perturbation theory. The resulting coupling constant curves were fitted to a cosine series with 8 coefficients. Our results are compared with those obtained previously and values estimated from experiment. It is found that the inclusion of electron correlation in the calculation of (3)JFF reduces the absolute values. This is mainly due to changes in the FC contribution, which for dihedral angles around the trans conformation even changes its sign. This sign change is responsible for the breakdown of the Karplus-like curve.
Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

PubMed Central

2016-01-01

Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757
4,4'-([4,4'-Bipyridine]-1,1'-diium-1,1'-diyl)dibenzoate dihydrate

DOE PAGES

Rodriguez, Mark A.; Sava Gallis, Dorina F.; Chavez, James S.; ...

2016-06-01

We report here the synthesis of a neutral viologen derivative, C 24H 16N 2O 4·2H 2O. The non-solvent portion of the structure (Z-Lig) is a zwitterion, consisting of two positively charged pyridinium cations and two negatively charged carboxylate anions. The carboxylate group is almost coplanar [dihedral angle = 2.04 (11)°] with the benzene ring, whereas the dihedral angle between pyridine and benzene rings is 46.28 (5)°. TheZ-Lig molecule is positioned on a center of inversion (Fig. 1). The presence of the twofold axis perpendicular to thec-glide plane in space groupC2/c generates a screw-axis parallel to thebaxis that is shifted from themore » origin by 1/4 in theaandcdirections. This screw-axis replicates the molecule (and solvent water molecules) through space. TheZ-Lig molecule links to adjacent moleculesviaO—H...O hydrogen bonds involving solvent water molecules as well as intermolecular C—H...O interactions. There are also π–π interactions between benzene rings on adjacent molecules.« less
Characterization, photophysical and DFT calculation study on 2-(2,4-difluorophenyl)-1-(4-methoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline ligand.

PubMed

Jayabharathi, Jayaraman; Thanikachalam, Venugopal; Venkatesh Perumal, Marimuthu

2012-09-01

The synthesized imidazole derivative 2-(2,4-difluorophenyl)-1-(4-methoxyphenyl)-1H-imidazo[4,5-f][1,10] phenanthroline (dfpmpip) has been characterized using IR, mass, (1)H, (13)C NMR and elemental analysis. The photophysical properties of dfpmpip have been studied using UV-visible and fluorescence spectroscopy in different solvents. The solvent effect on the absorption and fluorescence bands has been analyzed by a multi-component linear regression. Theoretically calculated bond lengths, bond angles and dihedral angles are found to be slightly higher than that of X-ray Diffraction (XRD) values of its parent compound. The charge distribution has been calculated from the atomic charges by non-linear optical (NLO) and natural bond orbital (NBO) analysis. Since the synthesized imidazole derivative has the largest μ(g)β(0) value, the reported imidazole can be used as potential NLO material. The energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) levels and the molecular electrostatic potential (MEP) energy surface studies evidenced the existence of intramolecular charge transfer (ICT) within the molecule. Theoretical calculations regarding the chemical potential (μ), hardness (η) and electrophilicity index (ω) have also been calculated. Copyright © 2012 Elsevier B.V. All rights reserved.
Validation of nuclear magnetic resonance structures of proteins and nucleic acids: hydrogen geometry and nomenclature.

PubMed

Doreleijers, J F; Vriend, G; Raves, M L; Kaptein, R

1999-11-15

A statistical analysis is reported of 1,200 of the 1,404 nuclear magnetic resonance (NMR)-derived protein and nucleic acid structures deposited in the Protein Data Bank (PDB) before 1999. Excluded from this analysis were the entries not yet fully validated by the PDB and the more than 100 entries that contained < 95% of the expected hydrogens. The aim was to assess the geometry of the hydrogens in the remaining structures and to provide a check on their nomenclature. Deviations in bond lengths, bond angles, improper dihedral angles, and planarity with respect to estimated values were checked. More than 100 entries showed anomalous protonation states for some of their amino acids. Approximately 250,000 (1.7%) atom names differed from the consensus PDB nomenclature. Most of the inconsistencies are due to swapped prochiral labeling. Large deviations from the expected geometry exist for a considerable number of entries, many of which are average structures. The most common causes for these deviations seem to be poor minimization of average structures and an improper balance between force-field constraints for experimental and holonomic data. Some specific geometric outliers are related to the refinement programs used. A number of recommendations for biomolecular databases, modeling programs, and authors submitting biomolecular structures are given.
(E)-1,2-Bis(4-fluorophenyl)ethane-1,2-dione

PubMed Central

Fun, Hoong-Kun; Kia, Reza

2008-01-01

The title compound, C14H8F2O2, is a substituted benzil with an s-trans conformation of the dicarbonyl unit. This conformation is also shown by the O—C—C—O torsion angle of −110.65 (12)°. An unusual feature of the structure is the length, 1.536 (2) Å, of the central C—C bond connecting the carbonyl units, which is significantly longer than a normal Csp 2—Csp 2 single bond. This is probably the result of decreasing the unfavourable vicinal dipole–dipole interactions by increasing the distance between the two electronegative O atoms [O⋯O = 3.1867 (12) Å] and allowing orbital overlap of the dione with the π system of the benzene rings. The dihedral angle between the aromatic rings is 64.74 (5)°. In the crystal structure, neighbouring molecules are linked together by weak intermolecular C—H⋯O (× 2) hydrogen bonds. In addition, the crystal structure is further stabilized by intermolecular π–π interactions with centroid–centroid distances in the range 3.6416 (6)–3.7150 (7) Å. PMID:21203308
4-(Naphthalene-2-carboxamido)pyridin-1-ium thiocyanate–N-(pyridin-4-yl)naphthalene-2-carboxamide (1/1)

PubMed Central

Saeed, Sohail; Rashid, Naghmana; Butcher, Ray J.; Öztürk Yildirim, Sema; Hussain, Rizwan

2012-01-01

The asymmetric unit of the title compound, C16H13N2O+·NCS−·C16H12N2O, contains two N-(pyridin-4-yl)naphthalene-2-carboxamide molecules, both are partially protonated in the pyridine moiety, i.e. the H atom attached to the pyridine N atom is partially occupied with an occupancy factor of 0.61 (3) and 0.39 (3), respectively. In the crystal, protonated and neutral N-(pyridin-4-yl)naphthalene-2-carboxamide molecules are linked by N—H⋯N hydrogen bonding; the thiocyanate counter-ion links with both protonated and neutral N-(pyridin-4-yl)naphthalene-2-carboxamide molecules via N—H⋯S and N—H⋯N hydrogen bonding. The dihedral angles between the pyridine ring and naphthalene ring systems are 11.33 (6) and 9.51 (6)°, respectively. π–π stacking is observed in the crystal structure, the shortest centroid–centroid distance being 3.5929 (8) Å. The crystal structure was determined from a nonmerohedral twin {ratio of the twin components = 0.357 (1):0.643 (1) and twin law [-100 0-10 -101]}. PMID:23125774
Microstructural evidence of melting in crustal rocks (Invited)

NASA Astrophysics Data System (ADS)

Holness, M. B.; Cesare, B.; Sawyer, E. W.

2010-12-01

The signature of the former presence of melt on a microscopic scale is highly variable, subject to modification both during the melting event and during its subsequent history. Static pyrometamorphism results in melt films on grain boundaries between reactant phases. If a volume increase is involved, melting results in hydrofracture. On a longer timescale, as demonstrated by fragments of the crustal source in lava flows at El Hoyazo (SE Spain), melt occurs throughout the rock. These examples are highly unusual: the great majority of rocks that underwent melting cooled more slowly, permitting microstructural modification driven by a combination of textural equilibration, reaction and deformation. In the absence of deformation, and at constant temperature, melt-bearing rocks approach textural equilibrium, characterised by uniform grain size, smoothly curved grain boundaries and the establishment at all three-grain junctions of the equilibrium dihedral angle. The dihedral angle controls melt connectivity, with consequences for melt mobility and rock rheology. However, deformation is the rule rather than the exception in regional metamorphic terrains with profound effects on melt distribution. If deformation occurs predominantly by diffusive processes, textural equilibration can keep pace. At higher deformation rates melt is squeezed into planar pockets aligned parallel to the shearing direction or perpendicular to the extensional stress. Microstructures formed during solidification are controlled by cooling rate, H2O, and the size of the melt pockets. Large pockets solidify to look like igneous rocks. In small pores the supersaturation required for crystal growth is high and melt persist to lower temperatures, even being preserved as tiny glassy inclusions (“nanogranites”) in regional terranes. The pore size effect changes crystallization order, resulting in small, highly cuspate grains on grain boundaries with low dihedral angles. Crystallisation microstructures of poly-component liquids are highly dependent on diffusion rates, and therefore H2O content. Dry conditions result in diffusion-limited crystallisation to form intergrowths and symplectites (e.g. granophyre). The cooling rate must be slow in order to nucleate and grow individual grains from the melt. If the melt was primarily concentrated in thick films on grain boundaries this results in the “string of beads” texture. If there is sufficient water, and the rocks stay sufficiently hot, the microstructures will move towards a granular texture, driven by the reduction in interfacial energy. Highly cuspate pseudomorphs of melt at three-grain junctions will become rounded as the dihedral angle increases (generally towards the range 110-140°). Melt-related microstructures are more likely to be retained in dry rocks: in migmatite terranes in which melting was driven by infiltration of aqueous fluids and where melt extraction wasn’t pervasive, microstructures are likely to have been significantly modified by sub-solidus recrystallisation, especially likely if the rock underwent intense deformation on the retrograde path.

N-(4-Meth-oxy-phen-yl)-6-methyl-2-phenyl-5-{[4-(tri-fluoro-meth-yl)anilino]meth-yl}pyrimidin-4-amine.

PubMed

Cieplik, Jerzy; Pluta, Janusz; Bryndal, Iwona; Lis, Tadeusz

2013-11-27

The title compound, C26H23F3N4O, crystallizes with two symmetry-independent mol-ecules in the asymmetric unit, denoted A and B, which differ mainly in the rotation of the meth-oxy-phenyl ring. The -CF3 group of mol-ecule B is disordered by rotation, with the F atoms split over two sets of sites; the occupancy factor for the major component is 0.853 (4). The dihedral angles between the pyrimidine ring and the attached phenyl, meth-oxy-phenyl and tri-fluoro-methyl-phenyl rings are 8.1 (2), 37.5 (2) and 70.7 (2)°, respectively, in mol-ecule A, and 9.3 (2), 5.3 (2) and 79.7 (2)° in mol-ecule B. An intra-molecular N-H⋯N hydrogen bond occurs in each mol-ecule. In the crystal, two crystallographically independent mol-ecules associate into a dimer via a pair of N-H⋯N hydrogen bonds, with a resulting R 2 (2)(12) ring motif and π-π stacking inter-actions [centroid-centroid distance = 3.517 (4) Å] between the pyrimidine rings. For the A mol-ecules, there are inter-molecular C-H⋯O hydrogen bonds between an aryl C atom of meth-oxy-phenyl ring and a meth-oxy O atom of an adjacent mol-ecule. A similar inter-action is lacking in the B mol-ecules.
New Coarse-Grained Model and Its Implementation in Simulations of Graphene Assemblies.

PubMed

Shang, Jun-Jun; Yang, Qing-Sheng; Liu, Xia

2017-08-08

Graphene is a one-atom thick layer of carbon atoms arranged in a hexagonal pattern, which makes it the strongest material in the world. The Tersoff potential is a suitable potential for simulating the mechanical behavior of the complex covalently bonded system of graphene. In this paper, we describe a new coarse-grained (CG) potential, TersoffCG, which is based on the function form of the Tersoff potential. The TersoffCG applies to a CG model of graphene that uses the same hexagonal pattern as the atomistic model. The parameters of the TersoffCG potential are determined using structural feature and potential-energy fitting between the CG model and the atomic model. The modeling process of graphene is highly simplified using the present CG model as it avoids the necessity to define bonds/angles/dihedrals connectivity. What is more, the present CG model provides a new perspective of coarse-graining scheme for crystal structures of nanomaterials. The structural changes and mechanical properties of multilayer graphene were calculated using the new potential. Furthermore, a CG model of a graphene aerogel was built in a specific form of assembly. The chemical bonding in the joints of graphene-aerogel forms automatically during the energy relaxation process. The compressive and recover test of the graphene aerogel was reproduced to study its high elasticity. Our computational examples show that the TersoffCG potential can be used for simulations of graphene and its assemblies, which have many applications in areas of environmental protection, aerospace engineering, and others.
Frequency Response of a Protein to Local Conformational Perturbations

PubMed Central

Eren, Dilek; Alakent, Burak

2013-01-01

Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B) was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD) potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as Cα atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >∼10×period of a perturbation cycle) not to be clouded by random diffusional fluctuations, and low enough (<∼0.8 ns−1) not to attenuate the propagating signal and enhance the contribution of the side-chains to the dissipation of the signals. Employing Discrete Fourier Transform (DFT) to TMD simulation trajectories of 16 cycles of conformational transitions at periods of 1.2 to 5 ns yielded Cα displacements consistent with those obtained from crystal structures. Identification of the perturbed atomic variables by statistical t-tests on log-log scale spectral densities revealed the extent of signal propagation in PTP1B, while phase angles of the filtered trajectories at the fundamental frequency were used to cluster collectively fluctuating elements. Hydrophobic interactions were found to have a higher contribution to signal transduction between side-chains compared to the role of polar interactions. Most of in-phase fluctuating residues on the signaling pathway were found to have high identity among PTP domains, and located over a wide region of PTP1B including the allosteric site. Due to its simplicity and efficiency, the suggested technique may find wide applications in identification of signaling pathways of different proteins. PMID:24086121
2-[(4-Benzhydrylpipérazin-1-yl)méthyl]acrylonitrile

PubMed Central

Ben Amor, Fatma; Ould M’hamed, Mohamed; Mrabet, Hédi; Driss, Ahmed; Efrit, Mohamed Lotfi

2008-01-01

In the title compound, 2-[(4-benzhydrylpiperazin-1-yl)methyl]acrylonitrile, C21H23N3, the substituted piperazine ring adopts a chair conformation and the dihedral angle between the mean planes of the aromatic rings is 71.61 (8)°. PMID:21201087
4-Dimethylamino-N′-(2-methoxybenzylidene)benzohydrazide

PubMed Central

Su, Fu; Gu, Zheng-Gui; Lin, Jun

2011-01-01

In the title molecule, C17H19N3O2, the dihedral angle between the two benzene rings is 14.05 (15)°. In the crystal, molecules are linked through intermolecular N—H⋯O hydrogen bonds, forming chains along b. PMID:22090947
4-[(3-Chloro-2-methylphenyl)iminomethyl]phenol

PubMed Central

Manjunath, B. C.; Abdoh, M. M. M; Mallesha, L.; Mohana, K. N.; Lokanath, N. K.

2012-01-01

In the title compound, C14H12ClNO, the dihedral angle between the aromatic rings is 39.84 (7)°. In th crystal, molecules are connected by O—H⋯N hydrogen bonds into chains parallel to [001]. In addition, a C—H⋯π contact occurs. PMID:23284502
4,5-Dibromo-2,7-di-tert-butyl-9,9-dimethyl-9H-thioxanthene

PubMed Central

Rubio, Omayra H.; Fuentes de Arriba, Angel L.; Sanz, Francisca; Muniz, Francisco M.; Morán, Joaquín R.

2012-01-01

In the title compound, C23H28Br2S, the thioxanthene unit is twisted, showing a dihedral angle of 29.3 (5)° between the benzene rings. When projected along [001], the packing shows two types of channels. The crystal studied was a racemic twin. PMID:22719586
(2-{[2-(diphenyl-phosphino)phen-yl]thio}-phen-yl)diphenyl-phosphine sulfide.

PubMed

Alvarez-Larena, Angel; Martinez-Cuevas, Francisco J; Flor, Teresa; Real, Juli

2012-11-01

In the title compound, C(36)H(28)P(2)S(2), the dihedral angle between the central benzene rings is 66.95 (13)°. In the crystal, molecules are linked via C(ar)-H⋯π and π-π inter-actions [shortest centroid-centroid distance between benzene rings = 3.897 (2) Å].
Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.

PubMed Central

Mathiowetz, A. M.; Goddard, W. A.

1995-01-01

Dihedral probability grid Monte Carlo (DPG-MC) is a general-purpose method of conformational sampling that can be applied to many problems in peptide and protein modeling. Here we present the DPG-MC method and apply it to predicting complete protein structures from C alpha coordinates. This is useful in such endeavors as homology modeling, protein structure prediction from lattice simulations, or fitting protein structures to X-ray crystallographic data. It also serves as an example of how DPG-MC can be applied to systems with geometric constraints. The conformational propensities for individual residues are used to guide conformational searches as the protein is built from the amino-terminus to the carboxyl-terminus. Results for a number of proteins show that both the backbone and side chain can be accurately modeled using DPG-MC. Backbone atoms are generally predicted with RMS errors of about 0.5 A (compared to X-ray crystal structure coordinates) and all atoms are predicted to an RMS error of 1.7 A or better. PMID:7549885
Probabilistic models for capturing more physicochemical properties on protein-protein interface.

PubMed

Guo, Fei; Li, Shuai Cheng; Du, Pufeng; Wang, Lusheng

2014-06-23

Protein-protein interactions play a key role in a multitude of biological processes, such as signal transduction, de novo drug design, immune responses, and enzymatic activities. It is of great interest to understand how proteins interact with each other. The general approach is to explore all possible poses and identify near-native ones with the energy function. The key issue here is to design an effective energy function, based on various physicochemical properties. In this paper, we first identify two new features, the coupled dihedral angles on the interfaces and the geometrical information on π-π interactions. We study these two features through statistical methods: a mixture of bivariate von Mises distributions is used to model the correlation of the coupled dihedral angles, while a mixture of bivariate normal distributions is used to model the orientation of the aromatic rings on π-π interactions. Using 6438 complexes, we parametrize the joint distribution of each new feature. Then, we propose a novel method to construct the energy function for protein-protein interface prediction, which includes the new features as well as the existing energy items such as dDFIRE energy, side-chain energy, atom contact energy, and amino acid energy. Experiments show that our method outperforms the state-of-the-art methods, ZRANK and ClusPro. We use the CAPRI evaluation criteria, Irmsd value, and Fnat value. On Benchmark v4.0, our method has an average Irmsd value of 3.39 Å and Fnat value of 62%, which improves upon the average Irmsd value of 3.89 Å and Fnat value of 49% for ZRANK, and the average Irmsd value of 3.99 Å and Fnat value of 46% for ClusPro. On the CAPRI targets, our method has an average Irmsd value of 3.56 Å and Fnat value of 42%, which improves upon the average Irmsd value of 4.27 Å and Fnat value of 39% for ZRANK, the average Irmsd value of 5.15 Å and Fnat value of 30% for ClusPro.
Fast equilibration protocol for million atom systems of highly entangled linear polyethylene chains

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

Sliozberg, Yelena R.; TKC Global, Inc., Aberdeen Proving Ground, Maryland 21005; Kröger, Martin

Equilibrated systems of entangled polymer melts cannot be produced using direct brute force equilibration due to the slow reptation dynamics exhibited by high molecular weight chains. Instead, these dense systems are produced using computational techniques such as Monte Carlo-Molecular Dynamics hybrid algorithms, though the use of soft potentials has also shown promise mainly for coarse-grained polymeric systems. Through the use of soft-potentials, the melt can be equilibrated via molecular dynamics at intermediate and long length scales prior to switching to a Lennard-Jones potential. We will outline two different equilibration protocols, which use various degrees of information to produce the startingmore » configurations. In one protocol, we use only the equilibrium bond angle, bond length, and target density during the construction of the simulation cell, where the information is obtained from available experimental data and extracted from the force field without performing any prior simulation. In the second protocol, we moreover utilize the equilibrium radial distribution function and dihedral angle distribution. This information can be obtained from experimental data or from a simulation of short unentangled chains. Both methods can be used to prepare equilibrated and highly entangled systems, but the second protocol is much more computationally efficient. These systems can be strictly monodisperse or optionally polydisperse depending on the starting chain distribution. Our protocols, which utilize a soft-core harmonic potential, will be applied for the first time to equilibrate a million particle system of polyethylene chains consisting of 1000 united atoms at various temperatures. Calculations of structural and entanglement properties demonstrate that this method can be used as an alternative towards the generation of entangled equilibrium structures.« less
Crystal structure of a mononuclear Ru(II) complex with a back-to-back terpyridine ligand: [RuCl(bpy)(tpy-tpy)](.).

PubMed

Rein, Francisca N; Chen, Weizhong; Scott, Brian L; Rocha, Reginaldo C

2015-09-01

We report the structural characterization of [6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine](2,2'-bi-pyridine)-chlorido-ruthenium(II) hexa-fluorido-phosphate, [RuCl(C10H8N2)(C30H20N6)]PF6, which contains the bidentate ligand 2,2'-bi-pyridine (bpy) and the tridendate ligand 6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine (tpy-tpy). The [RuCl(bpy)(tpy-tpy)](+) monocation has a distorted octa-hedral geometry at the central Ru(II) ion due to the restricted bite angle [159.32 (16)°] of the tridendate ligand. The Ru-bound tpy and bpy moieties are nearly planar and essentially perpendicular to each other with a dihedral angle of 89.78 (11)° between the least-squares planes. The lengths of the two Ru-N bonds for bpy are 2.028 (4) and 2.075 (4) Å, with the shorter bond being opposite to Ru-Cl. For tpy-tpy, the mean Ru-N distance involving the outer N atoms trans to each other is 2.053 (8) Å, whereas the length of the much shorter bond involving the central N atom is 1.936 (4) Å. The Ru-Cl distance is 2.3982 (16) Å. The free uncoordinated moiety of tpy-tpy adopts a trans,trans conformation about the inter-annular C-C bonds, with adjacent pyridyl rings being only approximately coplanar. The crystal packing shows significant π-π stacking inter-actions based on tpy-tpy. The crystal structure reported here is the first for a tpy-tpy complex of ruthenium.
Solution structure of an artificial Fe8S8 ferredoxin: the D13C variant of Bacillus schlegelii Fe7S8 ferredoxin.

PubMed

Aono, S; Bentrop, D; Bertini, I; Cosenza, G; Luchinat, C

1998-12-01

The solution structure of the D13C variant of the thermostable Fe7S8 ferredoxin from Bacillus schlegelii has been determined by 1H-NMR spectroscopy in its oxidized form. In a variable-temperature NMR study the D13C variant was as thermostable (up to 90 degrees C) as the wild-type protein (WT). Seventy-five out of 77 amino acid residues and 81% of all theoretically expected proton resonances in the D13C Fe8S8 protein have been assigned. Its structure was determined through torsion angle dynamics calculations with the program DYANA, using 935 meaningful NOEs (from a total of 1251), hydrogen bond constraints, and NMR-derived dihedral angle constraints for the cluster-ligating cysteines. Afterwards, restrained energy minimization and restrained molecular dynamics were applied to each conformer of the family. The final family of 20 structures has RMSD values from the mean structure of 0.055 nm for the backbone atoms and of 0.099 nm for all heavy atoms. The overall folding of the WT is maintained in the mutant, except for the immediate vicinity of the new cysteine, which becomes much more similar to native Fe8S8 proteins. The two residues at positions 11 and 12, which constitute an insertion with respect to all known Fe8S8 proteins, assume a conformation that does not prevent the preceding and following residues from folding like in native Fe8S8 proteins. Clear evidence for the existence of two conformations involving almost half of the amino acid residues was found. The two conformations are structurally indistinguishable. Temperature-dependent NMR experiments show that one of them is thermodynamically more stable than the other.
Magnetic exchange in {Gd(III)-radical} complexes: method assessment, mechanism of coupling and magneto-structural correlations.

PubMed

Gupta, Tulika; Rajeshkumar, Thayalan; Rajaraman, Gopalan

2014-07-28

Density functional studies have been performed on ten different {Gd(III)-radical} complexes exhibiting both ferro and antiferromagnetic exchange interaction with an aim to assess a suitable exchange-correlation functional within DFT formalism. This study has also been extended to probe the mechanism of magnetic coupling and to develop suitable magneto-structural correlations for this pair. Our method assessments reveal the following order of increasing accuracy for the evaluation of J values compared to experimental coupling constants: B(40HF)LYP < BHandHLYP < TPSSH < PW91 < PBE < BP86 < OLYP < BLYP < PBE0 < X3LYP < B3LYP < B2PLYP. Grimme's double-hybrid functional is found to be superior compared to other functionals tested and this is followed very closely by the conventional hybrid B3LYP functional. At the basis set front, our calculations reveal that the incorporation of relativistic effect is important in these calculations and the relativistically corrected effective core potential (ECP) basis set is found to yield better Js compared to other methods. The supposedly empty 5d/6s/6p orbitals of Gd(III) are found to play an important role in the mechanism of magnetic coupling and different contributions to the exchange terms are probed using Molecular Orbital (MO) and Natural Bond Orbital (NBO) analysis. Magneto-structural correlations for Gd-O distances, Gd-O-N angles and Gd-O-N-C dihedral angles are developed where the bond angles as well as dihedral angle parameters are found to dictate the sign and strength of the magnetic coupling in this series.
Improved treatment of nucleosides and nucleotides in the OPLS-AA force field

NASA Astrophysics Data System (ADS)

Robertson, Michael J.; Tirado-Rives, Julian; Jorgensen, William L.

2017-09-01

DFT calculations have been used to develop improved descriptions of the torsional energetics for nucleosides and nucleotides in the OPLS-AA force field. Scans of nucleotide dihedral angles (γ, χ, and β) and methyl phosphates provided the bases for the new torsional parameters. In addition, the angle-bending parameters of phosphodiesters and ribose were updated, and adjustments were made to existing carbohydrate torsions to better capture the sugar puckering landscape of ribose. MD simulations of nucleosides with the new parameters demonstrate a significant improvement in the ribose sugar puckering and χ angle distributions. Additionally, energy-minimization of protein-nucleotide crystal structures with the new parameters produced accurate poses.
Computational Study of Environmental Effects on Torsional Free Energy Surface of N-Acetyl-N'-methyl-L-alanylamide Dipeptide

ERIC Educational Resources Information Center

Carlotto, Silvia; Zerbetto, Mirco

2014-01-01

We propose an articulated computational experiment in which both quantum mechanics (QM) and molecular mechanics (MM) methods are employed to investigate environment effects on the free energy surface for the backbone dihedral angles rotation of the small dipeptide N-Acetyl-N'-methyl-L-alanylamide. This computation exercise is appropriate for an…
(E)-4-{[(Pyridin-4-ylmethylidene)amino]methyl}benzoic acid

PubMed Central

Han, Sun Hwa; Lee, Soon W.

2012-01-01

The title molecule, C14H12N2O2, exhibits a V-shaped conformation with a dihedral angle of 59.69 (3)° between the benzene and pyridine rings. In the crystal, O—H⋯N hydrogen bonds link the molecules into zigzag chains along [010]. PMID:22346932
N-Crotylphthalimide

PubMed Central

Flores-Alamo, Marcos; del Carmen Romero-Quiroz, María; Morgado, Jorge

2010-01-01

In the title compound {systematic name: 2-[(E)-but-2-en-1-yl]isoindoline-1,3-dione}, C12H11NO2, the phthalimide ring system is essentially planar, with a maximum deviation of 0.008 (1) Å, while the plane of the N-crotyl substituent is orthogonal to the phthalimide ring system, making a dihedral angle of 87.5 (1)°. PMID:21589502
1,1′-Bicyclopropyl-1,1′-diyl 1,1′-biphenyl-2,2′-dicarboxylate

PubMed Central

Fun, Hoong-Kun; Quah, Ching Kheng; Xu, Kai

2012-01-01

In the title compound, C20H16O4, the two benzene rings form a dihedral angle of 45.70 (4)°. In the crystal, molecules are linked via C—H⋯O interactions into layers lying parallel to the bc plane. PMID:22719433
(E)-3-(4-Chlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one

PubMed Central

Fun, Hoong-Kun; Chia, Tze Shyang; Sapnakumari, M.; Narayana, B.; Sarojini, B. K.

2012-01-01

In the title compound, C15H10ClFO, the fluoro-substituted benzene ring forms a dihedral angle of 44.41 (6)° with the chloro-substituted benzene ring. The only significant directional bonds in the crystal are weak C—H⋯π interactions. PMID:22412535

1-(Benzylideneamino)pyridinum iodide

PubMed Central

Cui, Yong-Tao; Wang, Jian-Qiang; Ji, Chun-Xiang; Wu, Cong-Ren; Guo, Cheng

2009-01-01

In the title compound, C12H11N2 +·I−, the aromatic rings are oriented at a dihedral angle of 73.40 (3)°. In the crystal structure, π–π contacts between the pyridine rings and the benzene and pyridine rings [centroid–centroid distances = 3.548 (3) and 4.211 (3) Å] may stabilize the structure. PMID:21581846
Quantum chemical determination of young?s modulus of lignin. Calculations on ß-O-4' model compound

Treesearch

Thomas Elder

2007-01-01

The calculation of Young?s modulus of lignin has been examined by subjecting a dimeric model compound to strain, coupled with the determination of energy and stress. The computational results, derived from quantum chemical calculations, are in agreement with available experimental results. Changes in geometry indicate that modifications in dihedral angles occur in...
1,5-Bis(1-phenylethylidene)thiocarbonohydrazide

PubMed Central

Feng, Lei; Ji, Haiwei; Wang, Renliang; Ge, Haiyan; Li, Li

2011-01-01

The title molecule, C17H18N4S, is not planar, as indicated by the dihedral angle of 27.24 (9)° between the two benzene rings. In the crystal, intermolecular N—H⋯S hydrogen bonds link pairs of molecules into inversion dimers. PMID:21754879
1,2,3-Triphenyl-1,2-dihydroquinoxaline

PubMed Central

Edelmann, Frank T.; Blaurock, Steffen; Lorenz, Volker; Fischer, Axel

2008-01-01

The title compound, C26H20N2, first reported in 1891, was obtained as a by-product in the preparation of benzildianil from benzil and excess aniline. The dihedral angles between the fused benzene ring and the pendant phenyl rings are 17.93 (11), 53.18 (10) and 89.08 (12)°. PMID:21201177
The balance of moments and the static longitudinal stability of airplanes

NASA Technical Reports Server (NTRS)

Muller, Horst

1929-01-01

A nomogram is developed which renders it possible by drawing a few lines, to determine: the location of the center of gravity for zero wing and tail moments; the longitudinal dihedral angle; the tail coefficient F(sub h) iota/F(sub t). Moreover there is no difficulty in determining the magnitude of the restoring moment or of the unstable moment.
The 2-Methoxy Group Orientation Regulates the Redox Potential Difference between the Primary (QA) and Secondary (QB) Quinones of Type II Bacterial Photosynthetic Reaction Centers.

PubMed

de Almeida, Wagner B; Taguchi, Alexander T; Dikanov, Sergei A; Wraight, Colin A; O'Malley, Patrick J

2014-08-07

Recent studies have shown that only quinones with a 2-methoxy group can act simultaneously as the primary (Q A ) and secondary (Q B ) electron acceptors in photosynthetic reaction centers from purple bacteria such as Rb. sphaeroides . 13 C HYSCORE measurements of the 2-methoxy group in the semiquinone states, SQ A and SQ B , were compared with DFT calculations of the 13 C hyperfine couplings as a function of the 2-methoxy dihedral angle. X-ray structure comparisons support 2-methoxy dihedral angle assignments corresponding to a redox potential gap (Δ E m ) between Q A and Q B of 175-193 mV. A model having a methyl group substituted for the 2-methoxy group exhibits no electron affinity difference. This is consistent with the failure of a 2-methyl ubiquinone analogue to function as Q B in mutant reaction centers with a Δ E m of ∼160-195 mV. The conclusion reached is that the 2-methoxy group is the principal determinant of electron transfer from Q A to Q B in type II photosynthetic reaction centers with ubiquinone serving as both acceptor quinones.
Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads

PubMed Central

Baruah, Anupaul; Rani, Pooja; Biswas, Parbati

2015-01-01

This work quantitatively characterizes intrinsic disorder in proteins in terms of sequence composition and backbone conformational entropy. Analysis of the normalized relative composition of the amino acid triads highlights a distinct boundary between globular and disordered proteins. The conformational entropy is calculated from the dihedral angles of the middle amino acid in the amino acid triad for the conformational ensemble of the globular, partially and completely disordered proteins relative to the non-redundant database. Both Monte Carlo (MC) and Molecular Dynamics (MD) simulations are used to characterize the conformational ensemble of the representative proteins of each group. The results show that the globular proteins span approximately half of the allowed conformational states in the Ramachandran space, while the amino acid triads in disordered proteins sample the entire range of the allowed dihedral angle space following Flory’s isolated-pair hypothesis. Therefore, only the sequence information in terms of the relative amino acid triad composition may be sufficient to predict protein disorder and the backbone conformational entropy, even in the absence of well-defined structure. The predicted entropies are found to agree with those calculated using mutual information expansion and the histogram method. PMID:26138206
Time-resolved fluorescence of thioredoxin single-tryptophan mutants: modeling experimental results with minimum perturbation mapping

NASA Astrophysics Data System (ADS)

Silva, Norberto D., Jr.; Haydock, Christopher; Prendergast, Franklyn G.

1994-08-01

The time-resolved fluorescence decay of single tryptophan (Trp) proteins is typically described using either a distribution of lifetimes or a sum of two or more exponential terms. A possible interpretation for this fluorescence decay heterogeneity is the existence of different isomeric conformations of Trp about its (chi) +1) and (chi) +2) dihedral angles. Are multiple Trp conformations compatible with the remainder of the protein in its crystallographic configuration or do they require repacking of neighbor side chains? It is conceivable that isomers of the neighbor side chains interconvert slowly on the fluorescence timescale and contribute additional lifetime components to the fluorescence intensity. We have explored this possibility by performing minimum perturbation mapping simulations of Trp 28 and Trp 31 in thioredoxin (TRX) using CHARMm 22. Mappings of Trp 29 and Trp 31 give the TRX Trp residue energy landscape as a function of (chi) +1) and (chi) +2) dihedral angles. Time-resolved fluorescence intensity and anisotropy decay of mutant TRX (W28F and W31F) are measured and interpreted in light of the above simulations. Relevant observables, like order parameters and isomerization rates, can be derived from the minimum perturbation maps and compared with experiment.
Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.

PubMed

Yang, Yi Isaac; Parrinello, Michele

2018-06-12

Collective variables are used often in many enhanced sampling methods, and their choice is a crucial factor in determining sampling efficiency. However, at times, searching for good collective variables can be challenging. In a recent paper, we combined time-lagged independent component analysis with well-tempered metadynamics in order to obtain improved collective variables from metadynamics runs that use lower quality collective variables [ McCarty, J.; Parrinello, M. J. Chem. Phys. 2017 , 147 , 204109 ]. In this work, we extend these ideas to variationally enhanced sampling. This leads to an efficient scheme that is able to make use of the many advantages of the variational scheme. We apply the method to alanine-3 in water. From an alanine-3 variationally enhanced sampling trajectory in which all the six dihedral angles are biased, we extract much better collective variables able to describe in exquisite detail the protein complex free energy surface in a low dimensional representation. The success of this investigation is helped by a more accurate way of calculating the correlation functions needed in the time-lagged independent component analysis and from the introduction of a new basis set to describe the dihedral angles arrangement.
Preliminary Heat-Transfer Measurements on a Hypersonic Glide Configuration Having 79.5 degree Sweepback and 45 degree Dihedral at a Mach Number of 4.95

NASA Technical Reports Server (NTRS)

Stainback, Calvin

1960-01-01

An experimental investigation was conducted to evaluate the heat-transfer characteristics of a hypersonic glide configuration having 79.5 deg of sweepback (measured in the plane of the leading edges) and 45 of dihedral. The tests were conducted at a nominal Mach number of 4.95 and a stagnation temperature of 400 F. The test-section unit Reynolds number was varied from 1.95 x 10(exp 6) to 12.24 x 10(exp 6) per foot. The results indicated that the laminar-flow heat-transfer rate to the lower surface of the model decreased as the distance from the ridge line increased except for thermocouples located near the semispan at an angle of attack of 00 with respect to the plane of the leading edges. The heat-transfer distribution (local heating rate relative to the ridge-line heating rate) was similar to the theoretical heat-transfer distribution for a two-dimensional blunt body, if the ridge line was assumed to be the stagnation line, and could be predicted by this theory provided a modified Newtonian pressure distribution was used. Except in the vicinity of the apex, the ridge-line heat-transfer rate could also be predicted from two-dimensional blunt-body heat-transfer theory provided it was assumed that the stagnation-line heat-transfer rate varied as the cosine of the effective sweep (sine of the angle of attack of the ridge line). The heat-transfer level on the lower surface and the nondimensional heat-transfer distribution around the body on the lower surface were in qualitative agreement with the results of a geometric study of highly swept delta wings with large positive dihedrals made in reference 1.
Characterization and comparison of perezone with some analogues. Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Escobedo-González, Rene Gerardo; Bahena, Luis; Arias Tellez, José Luis; Hinojosa Torres, Jaime; Ruvalcaba, Rene Miranda; Aceves-Hernández, Juan Manuel

2015-10-01

Perezone had been used for centuries in the traditional Mexican medicine, it is useful and a handful of illness. Perezone and other derivatives also present activity against certain lines of cancer, such as the myeloblastoid leukemia cell line K-562 and carcinoma cell lines (PC-3 and SKLU-1) with IC50 <10 μM. Perezone and isoperezone have shown the major cytotoxic potency. Characterization of perezone was carried out by UV-Visible, IR, DSC, TGA and powder X-ray diffraction, as well as docking studies using caspase-3 structures as receptors. Theoretical studies for optimizing the geometry of perezone were carried out and the results compared with values of single crystal X-ray diffraction. The experimental values of atomic distances, angles and dihedral angles are in good agreement with the theoretical values. Interaction of perezone with the cysteine catalytic site with the caspase-3 was found in the docking studies. A docking study of perezone, with horminone, thymoquinone and isoperezone as ligands and the protein apoptein, caspase-3 as receptor, was carried to demonstrate that the hindrance steric factor, chemical structure and the functional groups are important in the biological activity of these natural products. The docking score energetic values are in good agreement with the experimental cytotoxic results obtained from the experiments when perezone and analogues were studied in different types of cancer.
Crystal structure of 1-iodo-3-{[4-(tert-butylsulfanyl)phenyl]ethynyl}azulene

PubMed Central

Förster, Sebastian; Seichter, Wilhelm; Weber, Edwin

2015-01-01

The title compound, C20H19IS, features a 1,3-disubstituted azulene involving an ethynylene elongated 4-(tert-butylsulfanyl)phenyl sidearm and an iodine atom as the substituents. The azulene ring system is almost planar (r.m.s. deviation = 0.012 Å) and subtends a dihedral angle of 35.7 (1)° with the benzene ring. As a result of the inherent dipole character of the azulene core, a supramolecular π–π dimer [separation between the centroids of the five- and seven-membered rings = 3.7632 (10) Å] with antiparallel orientated molecules can be observed in the crystal. The packing is consolidated by an unusual I⋯π(acetylene) contact [I⋯Cg = 3.34 Å, C—I⋯Cg = 173.3°], and a very weak C—H⋯π interaction is also found in the structure, with the azulene five-membered ring as the acceptor. PMID:26396788
Random close packing in protein cores

NASA Astrophysics Data System (ADS)

Ohern, Corey

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ ~ 0 . 75 , a value that is similar to close packing equal-sized spheres. A limitation of these analyses was the use of `extended atom' models, rather than the more physically accurate `explicit hydrogen' model. The validity of using the explicit hydrogen model is proved by its ability to predict the side chain dihedral angle distributions observed in proteins. We employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high resolution protein structures. We find that these protein cores have ϕ ~ 0 . 55 , which is comparable to random close-packing of non-spherical particles. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations and design of new functional proteins. We gratefully acknowledge the support of the Raymond and Beverly Sackler Institute for Biological, Physical, and Engineering Sciences, National Library of Medicine training grant T15LM00705628 (J.C.G.), and National Science Foundation DMR-1307712 (L.R.).
Vibrational spectra, DFT quantum chemical calculations and conformational analysis of P-iodoanisole.

PubMed

Arivazhagan, M; Anitha Rexalin, D; Geethapriya, J

2013-09-01

The solid phase FT-IR and FT-Raman spectra of P-iodoanisole (P-IA) have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by ab initio (HF) and density functional theory (B3LYP) methods with LanL2DZ as basis set. The potential energy surface scan for the selected dihedral angle of P-IA has been performed to identify stable conformer. The optimized structure parameters and vibrational wavenumbers of stable conformer have been predicted by density functional B3LYP method with LanL2DZ (with effective core potential representations of electrons near the nuclei for post-third row atoms) basis set. The nucleophilic and electrophilic sites obtained from the molecular electrostatic potential (MEP) surface were calculated. The temperature dependence of thermodynamic properties has been analyzed. Several thermodynamic parameters have been calculated using B3LYP with LanL2DZ basis set. Copyright © 2013 Elsevier B.V. All rights reserved.
Concerted dihedral rotations give rise to internal friction in unfolded proteins.

PubMed

Echeverria, Ignacia; Makarov, Dmitrii E; Papoian, Garegin A

2014-06-18

Protein chains undergo conformational diffusion during folding and dynamics, experiencing both thermal kicks and viscous drag. Recent experiments have shown that the corresponding friction can be separated into wet friction, which is determined by the solvent viscosity, and dry friction, where frictional effects arise due to the interactions within the protein chain. Despite important advances, the molecular origins underlying dry friction in proteins have remained unclear. To address this problem, we studied the dynamics of the unfolded cold-shock protein at different solvent viscosities and denaturant concentrations. Using extensive all-atom molecular dynamics simulations we estimated the internal friction time scales and found them to agree well with the corresponding experimental measurements (Soranno et al. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17800-17806). Analysis of the reconfiguration dynamics of the unfolded chain further revealed that hops in the dihedral space provide the dominant mechanism of internal friction. Furthermore, the increased number of concerted dihedral moves at physiological conditions suggest that, in such conditions, the concerted motions result in higher frictional forces. These findings have important implications for understanding the folding kinetics of proteins as well as the dynamics of intrinsically disordered proteins.
Theoretical antisymmetric span loading for wings of arbitrary plan form at subsonic speeds

NASA Technical Reports Server (NTRS)

Deyoung, John

1951-01-01

A simplified lifting-surface theory that includes effects of compressibility and spanwise variation of section lift-curve slope is used to provide charts with which antisymmetric loading due to arbitrary antisymmetric angle of attack can be found for wings having symmetric plan forms with a constant spanwise sweep angle of the quarter-chord line. Consideration is given to the flexible wing in roll. Aerodynamic characteristics due to rolling, deflected ailerons, and sideslip of wings with dihedral are considered. Solutions are presented for straight-tapered wings for a range of swept plan forms.
catena-Poly[bis(1,3-benzothiazol-3-ium) [[dichloridoantimonate(III)]-di-μ-chlorido-μ-oxido-[chloridoantimonate(III)]-μ-chlorido

PubMed Central

Chebout, Oussama; Boudraa, Mhamed; Bouacida, Sofiane; Merazig, Hocine; Boudaren, Chaouki

2016-01-01

The title compound, {(C7H6NS)2[Sb2Cl6O]}n, contains two benzothiazolidium cations and one tri-μ-chlorido-trichlorido-μ-oxido-diantimonate(III) anion. The structure of the inorganic cation may be described as as being built up from two polyhedra, i.e. a square-pyramidal SbCl4O and a distorted octahedral SbOCl5 unit, sharing a common face (comprising the O atom and two Cl atoms). The two benzothiazole cations are quasi-planar and subtend a dihedral angle of 19.93 (5)°. The crystal packing can be described by alternating (100) layers and [001] chains of the organic cations and inorganic anions connected through an extensive three-dimensional network of N—H⋯Cl, C—H⋯O and C—H⋯Cl hydrogen bonds. This is consolidated by slipped π–π stacking, with centroid-to-centroid distances between the benzothiazole rings of 3.7111 (18)–3.8452 (16) Å. These interactions link the molecules within the layers and also link the layers together and reinforce the cohesion of the ionic structure. PMID:26958390
2-(2,4-Dichlorophenyl)-2-oxoethyl 4-methoxybenzoate

PubMed Central

Fun, Hoong-Kun; Chia, Tze Shyang; Shenvi, Seema; Isloor, Arun M.; Garudachari, B.

2011-01-01

In the title compound, C16H12Cl2O4, the dihedral angle between the benzene rings is 70.11 (6)°. In the crystal, molecules are linked by C—H⋯O hydrogen bonds into a three-dimensional network. A C—H⋯π interaction is also observed. PMID:22199870
(Methyldiphenylphosphoranylidene)ammonium chloride

PubMed Central

Valerio-Cárdenas, Cintya; Ortiz-Frade, Luis; Grévy M., Jean-Michel

2009-01-01

The title compound, C13H15NP+·Cl−, was obtained by hydrolysis of the N-trimethysilyl derivative of methydiphenyliminophosphine. The dihedral angle between the phenyl rings in the cation is 61.5 (3)°. In the crystal structure, intermolecular N—H⋯Cl hydrogen bonds links the two components, forming a centrosymmetric 2 + 2 aggregate. PMID:21582794
(2-{[2-(diphenylphosphino)phenyl]thio}phenyl)diphenylphosphine sulfide

PubMed Central

Alvarez-Larena, Angel; Martinez-Cuevas, Francisco J.; Flor, Teresa; Real, Juli

2012-01-01

In the title compound, C36H28P2S2, the dihedral angle between the central benzene rings is 66.95 (13)°. In the crystal, molecules are linked via Car—H⋯π and π–π interactions [shortest centroid–centroid distance between benzene rings = 3.897 (2) Å]. PMID:23284423

1-(4-Chloro-2-fluoro-phen-yl)-4-difluoro-methyl-3-methyl-1H-1,2,4-triazol-5(4H)-one.

PubMed

Ren, Dong-Mei; Wang, Yong-Yi

2012-04-01

In the crystal structure of the title compound, C(10)H(7)ClF(3)N(3)O, pairs of mol-ecules are connected into dimers via pairs of C-H⋯O hydrogen bonds. The dihedral angle between the benzene ring and attached triazolone ring is 53.2 (1)°.
1-[1-(4-Chloro-phen-yl)ethyl-idene]carbono-hydrazide.

PubMed

Du, Lingyun; Du, Lei; Wang, Shuhao

2009-08-12

The mol-ecular skeleton of the title mol-ecule, C(9)H(11)ClN(4)O, is essentially planar, the dihedral angle between the ring and the and N/N/C plane being 6.7 (3)°. In the crystal, inter-molecular N-H⋯O and N-H⋯N hydrogen bonds link the mol-ecules into ribbons propagated along [010].
Development of Spacecraft Materials and Structures Fundamentals.

DTIC Science & Technology

1985-08-01

900. This is comparable to the dihedral angle observed in uranium dioxide’ ° and silicon carbide ,’ 2 which...necesjary and identify by bigich numberp FIELD GROUP I suB. GR. Boron carbide , sintering, grain growth, microstructure, microcracking, mechanical...Compacts of boron carbide powders with specific surface area >, 8 m2 / were sintered in argon at temperatures near 2200*C. Several of these powders were
Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer

PubMed Central

2015-01-01

Plexin-B1 is a single-pass transmembrane receptor. Its Rho GTPase binding domain (RBD) can associate with small Rho GTPases and can also self-bind to form a dimer. In total, more than 400 ns of NAMD molecular dynamics simulations were performed on RBD monomer and dimer. Different analysis methods, such as root mean squared fluctuation (RMSF), order parameters (S2), dihedral angle correlation, transfer entropy, principal component analysis, and dynamical network analysis, were carried out to characterize the motions seen in the trajectories. RMSF results show that after binding, the L4 loop becomes more rigid, but the L2 loop and a number of residues in other regions become slightly more flexible. Calculating order parameters (S2) for CH, NH, and CO bonds on both backbone and side chain shows that the L4 loop becomes essentially rigid after binding, but part of the L1 loop becomes slightly more flexible. Backbone dihedral angle cross-correlation results show that loop regions such as the L1 loop including residues Q25 and G26, the L2 loop including residue R61, and the L4 loop including residues L89–R91, are highly correlated compared to other regions in the monomer form. Analysis of the correlated motions at these residues, such as Q25 and R61, indicate two signal pathways. Transfer entropy calculations on the RBD monomer and dimer forms suggest that the binding process should be driven by the L4 loop and C-terminal. However, after binding, the L4 loop functions as the motion responder. The signal pathways in RBD were predicted based on a dynamical network analysis method using the pathways predicted from the dihedral angle cross-correlation calculations as input. It is found that the shortest pathways predicted from both inputs can overlap, but signal pathway 2 (from F90 to R61) is more dominant and overlaps all of the routes of pathway 1 (from F90 to P111). This project confirms the allosteric mechanism in signal transmission inside the RBD network, which was in part proposed in the previous experimental study. PMID:24901636
Space shuttle: Stability and control effectiveness of the MDAC parametric delta canard booster at Mach 0.38. Volume 1: Canard parametric variations

NASA Technical Reports Server (NTRS)

Bradley, D.; Buchholz, R. E.

1971-01-01

A 0.015 scale model of a modified version of the MDAC space shuttle booster was tested in the Naval Ship Research and Development Center 7 x 10 foot transonic wind tunnel, to obtain force, static stability, and control effectiveness data. Data were obtained for a cruise Mach Number of 0.38, altitude of 10,000 ft, and Reynolds Number per foot of approximately 2 x one million. The model was tested through an angle of attack range of -4 deg to 15 deg at zero degree angle of sideslip, and at an angle of sideslip range of -6 deg to 6 deg at fixed angles of attack of 0 deg, 6 deg, and 15 deg. Other test variables were elevon deflections, canard deflections, aileron deflections, rudder deflections, wing dihedral angle, canard incidence angle, wing incidence angle, canard position, wing position, wing and canard control flap size and dorsal fin size.
Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

NASA Astrophysics Data System (ADS)

Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

2017-01-01

This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.
(E)-1-(2-Aminophenyl)-3-(3,4,5-trimethoxyphenyl)prop-2-en-1-one

PubMed Central

Chantrapromma, Suchada; Ruanwas, Pumsak; Fun, Hoong-Kun

2011-01-01

In the asymmetric unit of the title chalcone derivative, C18H19NO4, there are three crystallographically independent molecules (molecules A, B and C). In molecule A, the dihedral angle between two benzene rings is 12.22 (10)° and the plane of the central prop-2-en-1-one unit makes dihedral angles of 11.02 (13) and 2.64 (12)° with the two adjacent benzene rings. The corresponding angles in molecule B are 12.35 (10), 18.78 (12) and 7.29 (12)°, respectively, and those in molecule C are 15.40 (10), 15.62 (3) and 3.19 (13)°. In each molecule, an intramolecular N—H⋯O hydrogen bond generates an S(6) ring motif. In the crystal structure, the molecules B are linked by intermolecular N—H⋯O hydrogen bonds into a zigzag chain along the c axis, while the molecules A and C are linked together via an N—H⋯O hydrogen bond into a dimer. Adjacent dimers are further connected by N—H⋯N hydrogen bonds into a three-dimensional network. Weak C—H⋯O and C—H⋯π interactions are also observed. PMID:22064816
The Effect of Mass Distribution on the Lateral Stability and Control Characteristics of an Airplane as Determined by Tests of a Model in the Free-Flight Tunnel

NASA Technical Reports Server (NTRS)

Seacord, Charles L; Campbell, John P.

1943-01-01

The effects of mass distribution on lateral stability and control characteristics of an airplane have been determined by flight tests of a model in the NACA free-flight tunnel. In the investigation, the rolling and yawing movements of inertia were increased from normal values to values up to five times normal. For each moment-of-inertia condition, combinations of dihedral and vertical-tail area representing a variety of airplane configurations were tested. The results of the flight tests of the model were correlated with calculated stability and control characteristics and, in general, good agreement was obtained. The tests showed the following effects of increased rolling and yawing moments of inertia: no appreciable change in spiral stability; reductions in oscillatory stability that were serious at high values of dihedral; a reduction in the sensitivity of the model to gust disturbances; and a reduction in rolling acceleration provided by the ailerons, which caused a marked increase in time to reach a given angle of bank. The general flight behavior of the model became worse with increasing moments of inertia but, with combinations of small effective dihedral and large vertical-tail area, satisfactory flight characteristics were obtained at all moment-of-inertia conditions.
Molecular structure, FT IR, NMR, UV, NBO and HOMO-LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311 ++G(d,2p) basis sets

NASA Astrophysics Data System (ADS)

Khajehzadeh, Mostafa; Moghadam, Majid

2017-06-01

Structural and molecular properties of antidepressants 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile were examined using quantum mechanics of Density Functional Theory (DFT)/B3LYP and PBEPBE methods with 6-311 ++ G(d,2p) and LanL2DZ basis sets to study the therapeutic properties of the drug. For this, the structure of desired material was optimized by the computer calculation method and with the use of powerful Gaussian 09 software. Then the lowest energy value and the bond length, bond angle and dihedral angle between its constituent atoms in the crystal structure of the desired material were measured from the optimized values. Then the amount of positive and negative charges, polarizability and dipole moment of its atoms using Mulliken charge and Natural atomic charges, DFT/B3LYP and PBEPBE methods with 6-311 ++ G(d,2p) and LanL2DZ basis sets were determined and the results were compared with each other for individual atoms and by mentioned methods. Also the type of stretching vibrations and bending vibrations between the constituent atoms of the molecule were specified using mentioned computational methods and FT IR vibrational spectra. The experimental spectrum of this material was taken to determine the functional groups and the computational and experimental values were compared to each other and Nuclear Magnetic Resonance (NMR) was used to specify the isomer shift between the carbons and protons in the presence of polar and nonpolar solvents. Also Natural Bond Orbital (NBO) was used to determine the type of electron transfers in σ → σ ∗ and π → π ∗ and LP(1) → σ ∗ and LP(2) → σ ∗ and the amount of hardness and softness in molecule was determined using the difference between ionization energy and electron affinity energy in constituent atoms of that molecule in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and in the presence of solvents H2O, CH3CN and C6H12. UV-Vis spectrum of the drug was taken using DFT/B3LYP and PBEPBE methods with 6-311 ++ G(d,2p) and LanL2DZ basis sets as well as solvents H2O, CH3CN and C6H12 and the associated transmissions were examined.
About crystal lattices and quasilattices in Euclidean space

NASA Astrophysics Data System (ADS)

Prokhoda, A. S.

2017-07-01

Definitions are given, based on which algorithms have been developed for constructing computer models of two-dimensional quasilattices and the corresponding quasiperiodic tilings in plane, the point symmetry groups of which are dihedral groups D m ( m = 5, 7, 8, 9, 10, 12, 14, 18), and the translation subgroups are free Abelian groups of the fourth or sixth rank. The angles at the tile vertices in the constructed tilings are calculated.
1-[6-(1H-Indol-1-yl)pyridin-2-yl]-1H-indole-3-carbaldehyde.

PubMed

Ramathilagam, C; Umarani, P R; Venkatesan, N; Rajakumar, P; Gunasekaran, B; Manivannan, V

2014-02-01

In the title compound, C22H15N3O, the dihedral angle between the two indole units is 33.72 (3)°. The mol-ecular structure features a weak intra-molecular C-H⋯N inter-action. In the crystal, weak C-H⋯O and C-H⋯π inter-actions, forming a two-dimensional network parallel to the bc plane.
3,3,6,6-Tetra-methyl-9-(2-nitro-phen-yl)-3,4,6,7-tetra-hydro-2H-xanthene-1,8(5H,9H)-dione.

PubMed

Mo, Yingming; Zang, Hong-Jun; Cheng, Bo-Wen

2010-07-31

In the title compound, C(23)H(25)NO(5), the pyran ring adopts a flattened boat conformation, while the two cyclo-hexenone rings are in envelope conformations. The 3-nitro-phenyl ring is almost perpendicular to the pyran ring, making a dihedral angle of 87.1 (3)°.
Sequence-specific unusual (1-->2)-type helical turns in alpha/beta-hybrid peptides.

PubMed

Prabhakaran, Panchami; Kale, Sangram S; Puranik, Vedavati G; Rajamohanan, P R; Chetina, Olga; Howard, Judith A K; Hofmann, Hans-Jörg; Sanjayan, Gangadhar J

2008-12-31

This article describes novel conformationally ordered alpha/beta-hybrid peptides consisting of repeating l-proline-anthranilic acid building blocks. These oligomers adopt a compact, right-handed helical architecture determined by the intrinsic conformational preferences of the individual amino acid residues. The striking feature of these oligomers is their ability to display an unusual periodic pseudo beta-turn network of nine-membered hydrogen-bonded rings formed in the forward direction of the sequence by 1-->2 amino acid interactions both in solid-state and in solution. Conformational investigations of several of these oligomers by single-crystal X-ray diffraction, solution-state NMR, and ab initio MO theory suggest that the characteristic steric and dihedral angle restraints exerted by proline are essential for stabilizing the unusual pseudo beta-turn network found in these oligomers. Replacing proline by the conformationally flexible analogue alanine (Ala) or by the conformationally more constrained alpha-amino isobutyric acid (Aib) had an adverse effect on the stabilization of this structural architecture. These findings increase the potential to design novel secondary structure elements profiting from the steric and dihedral angle constraints of the amino acid constituents and help to augment the conformational space available for synthetic oligomer design with diverse backbone structures.
Crystal structure of 3-{[4-(2-meth-oxy-phen-yl)piperazin-1-yl]meth-yl}-5-(thio-phen-2-yl)-1,3,4-oxa-diazole-2(3H)-thione.

PubMed

Al-Alshaikh, Monirah A; Abuelizz, Hatem A; El-Emam, Ali A; Abdelbaky, Mohammed S M; Garcia-Granda, Santiago

2016-02-01

The title compound, C18H20N4O2S2, is a new 1,3,4-oxa-diazole and a key pharmacophore of several biologically active agents. It is composed of a meth-yl(thio-phen-2-yl)-1,3,4-oxa-diazole-2(3H)-thione moiety linked to a 2-meth-oxy-phenyl unit via a piperazine ring that has a chair conformation. The thio-phene ring mean plane lies almost in the plane of the oxa-diazole ring, with a dihedral angle of 4.35 (9)°. The 2-meth-oxy-phenyl ring is almost normal to the oxa-diazole ring, with a dihedral angle of 84.17 (10)°. In the crystal, mol-ecules are linked by weak C-H⋯S hydrogen bonds and C-H⋯π inter-actions, forming layers parallel to the bc plane. The layers are linked via weak C-H⋯O hydrogen bonds and slipped parallel π-π inter-actions [inter-centroid distance = 3.6729 (10) Å], forming a three-dimensional structure. The thio-phene ring has an approximate 180° rotational disorder about the bridging C-C bond.
Two-Photon Absorption Properties of Gold Fluorescent Protein: A Combined Molecular Dynamics and Quantum Chemistry Study.

PubMed

Şimşek, Yusuf; Brown, Alex

2018-06-07

Molecular dynamics (MD) simulations were carried out to obtain the conformational changes of the chromophore in the gold fluorescent protein (PDB ID: 1OXF ). To obtain two-photon absorption (TPA) cross-sections, time dependent density functional theory (TD-DFT) computations were performed for chromophore geometries sampled along the trajectory. The TD-DFT computations used the CAM-B3LYP functional and 6-31+G(d) basis set. Results showed that two dihedral angles change remarkably over the simulation time. TPA cross-sections were found to average 13.82 GM for the excitation to S 1 computed from the equilibrium geometries; however, extending the structures with a water molecule and GLU residue, which make H bonds with the chromophore molecule, increased excitation energies and TPA cross-sections significantly. Besides the effects of the surrounding residues and the dihedrals on the spectroscopic properties, some bond lengths affected the excitation energies and the TPA cross-sections significantly (up to ±25-30%), while the effects of the bond angles were smaller (±5%). Overall the present results provide insight into the effects of the conformational flexibility on TPA (with gold fluorescent protein as a specific example) and suggest that further experimental measurements of TPA for the gold fluorescent protein should be undertaken.
Predicting side-chain conformations of methionine using a hard-sphere model with stereochemical constraints

NASA Astrophysics Data System (ADS)

Virrueta, A.; Gaines, J.; O'Hern, C. S.; Regan, L.

2015-03-01

Current research in the O'Hern and Regan laboratories focuses on the development of hard-sphere models with stereochemical constraints for protein structure prediction as an alternative to molecular dynamics methods that utilize knowledge-based corrections in their force-fields. Beginning with simple hydrophobic dipeptides like valine, leucine, and isoleucine, we have shown that our model is able to reproduce the side-chain dihedral angle distributions derived from sets of high-resolution protein crystal structures. However, methionine remains an exception - our model yields a chi-3 side-chain dihedral angle distribution that is relatively uniform from 60 to 300 degrees, while the observed distribution displays peaks at 60, 180, and 300 degrees. Our goal is to resolve this discrepancy by considering clashes with neighboring residues, and averaging the reduced distribution of allowable methionine structures taken from a set of crystallized proteins. We will also re-evaluate the electron density maps from which these protein structures are derived to ensure that the methionines and their local environments are correctly modeled. This work will ultimately serve as a tool for computing side-chain entropy and protein stability. A. V. is supported by an NSF Graduate Research Fellowship and a Ford Foundation Fellowship. J. G. is supported by NIH training Grant NIH-5T15LM007056-28.
Crystal structure of methyl (4R)-4-(4-meth-oxy-benzo-yl)-4-{[(1R)-1-phenyl-eth-yl]carbamo-yl}butano-ate.

PubMed

Manchado, Alejandro; Salgado, Mateo M; Vicente, Álvaro; Díez, David; Sanz, Francisca; Garrido, Narciso M

2017-04-01

The title compound, C 22 H 25 NO 5 , was prepared by CAN [cerium(IV) ammonium nitrate] oxidation of the corresponding β-lactam. The dihedral angle between the benzene rings is 13.3 (4)° and the C-N-C(=O)-C torsion angle is 176.1 (6)°. In the crystal, amide- C (4) N-H⋯O and reinforcing C-H⋯O hydrogen bonds link the mol-ecules into infinite [010] chains. Further C-H⋯O hydrogen bonds cross-link the chains in the c -axis direction.
An experimental investigation of an oblique-wing and body combination at Mach numbers between 0.60 and 1.40

NASA Technical Reports Server (NTRS)

Graham, L. A.; Jones, R. T.; Boltz, F. W.

1972-01-01

An experimental investigation was conducted in an 11- by 11-foot wind tunnel to determine the aerodynamic characteristics of an oblique high aspect ratio wing in combination with a high fineness-ratio Sears-Haack body. Longitudinal and lateral-directional stability data were obtained at wing yaw angles from 0 deg to 60 deg over a test Mach number range from 0.6 to 1.4 for angles of attack between minus 6 deg and 9 deg. The effects of changes in Reynolds number, dihedral, and trailing-edge angle were studied along with the effects of a roughness strip on the upper and lower surfaces of the wing. Flow-visualization studies were made to determine the nature of the flow on the wing surfaces.
Wind-tunnel static and free-flight investigation of high-angle-of-attack stability and control characteristics of a model of the EA-6B airplane

NASA Technical Reports Server (NTRS)

Jordan, Frank L., Jr.; Hahne, David E.

1992-01-01

An investigation was conducted in the Langley 30- by 60-Foot Tunnel and the Langley 12-Foot Low-Speed Tunnel to identify factors contributing to a directional divergence at high angles of attack for the EA-6B airplane. The study consisted of static wind-tunnel tests, smoke and tuft flow-visualization tests, and free-flight tests of a 1/8.5-scale model of the airplane. The results of the investigation indicate that the directional divergence of the airplane is brought about by a loss of directional stability and effective dihedral at high angles of attack. Several modifications were tested that significantly alleviate the stability problem. The results of the free-flight study show that the modified configuration exhibits good dynamic stability characteristics and could be flown at angles of attack significantly higher than those of the unmodified configuration.
Perturbational formulation of principal component analysis in molecular dynamics simulation.

PubMed

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

2008-10-01

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, several versions of PCA, such as Cartesian coordinate PCA and dihedral angle PCA (dPCA), are limited to use with molecules with a single dominant state or proteins where the dihedral angle represents an important internal coordinate. Other PCAs with general applicability, such as the PCA using pairwise atomic distances, do not represent the physical meaning clearly. Therefore, a formulation that provides general applicability and clearly represents the physical meaning is yet to be developed. For developing such a formulation, we consider the conformational distribution change by the perturbation with arbitrary linearly independent perturbation functions. Within the second order approximation of the Kullback-Leibler divergence by the perturbation, the PCA can be naturally interpreted as a method for (1) decomposing a given perturbation into perturbations that independently contribute to the conformational distribution change or (2) successively finding the perturbation that induces the largest conformational distribution change. In this perturbational formulation of PCA, (i) the eigenvalue measures the Kullback-Leibler divergence from the unperturbed to perturbed distributions, (ii) the eigenvector identifies the combination of the perturbation functions, and (iii) the principal component determines the probability change induced by the perturbation. Based on this formulation, we propose a PCA using potential energy terms, and we designate it as potential energy PCA (PEPCA). The PEPCA provides both general applicability and clear physical meaning. For demonstrating its power, we apply the PEPCA to an alanine dipeptide molecule in vacuum as a minimal model of a nonsingle dominant conformational biomolecule. The first and second principal components clearly characterize two stable states and the transition state between them. Positive and negative components with larger absolute values of the first and second eigenvectors identify the electrostatic interactions, which stabilize or destabilize each stable state and the transition state. Our result therefore indicates that PCA can be applied, by carefully selecting the perturbation functions, not only to identify the molecular conformational fluctuation but also to predict the conformational distribution change by the perturbation beyond the limitation of the previous methods.

Perturbational formulation of principal component analysis in molecular dynamics simulation

NASA Astrophysics Data System (ADS)

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

2008-10-01

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, several versions of PCA, such as Cartesian coordinate PCA and dihedral angle PCA (dPCA), are limited to use with molecules with a single dominant state or proteins where the dihedral angle represents an important internal coordinate. Other PCAs with general applicability, such as the PCA using pairwise atomic distances, do not represent the physical meaning clearly. Therefore, a formulation that provides general applicability and clearly represents the physical meaning is yet to be developed. For developing such a formulation, we consider the conformational distribution change by the perturbation with arbitrary linearly independent perturbation functions. Within the second order approximation of the Kullback-Leibler divergence by the perturbation, the PCA can be naturally interpreted as a method for (1) decomposing a given perturbation into perturbations that independently contribute to the conformational distribution change or (2) successively finding the perturbation that induces the largest conformational distribution change. In this perturbational formulation of PCA, (i) the eigenvalue measures the Kullback-Leibler divergence from the unperturbed to perturbed distributions, (ii) the eigenvector identifies the combination of the perturbation functions, and (iii) the principal component determines the probability change induced by the perturbation. Based on this formulation, we propose a PCA using potential energy terms, and we designate it as potential energy PCA (PEPCA). The PEPCA provides both general applicability and clear physical meaning. For demonstrating its power, we apply the PEPCA to an alanine dipeptide molecule in vacuum as a minimal model of a nonsingle dominant conformational biomolecule. The first and second principal components clearly characterize two stable states and the transition state between them. Positive and negative components with larger absolute values of the first and second eigenvectors identify the electrostatic interactions, which stabilize or destabilize each stable state and the transition state. Our result therefore indicates that PCA can be applied, by carefully selecting the perturbation functions, not only to identify the molecular conformational fluctuation but also to predict the conformational distribution change by the perturbation beyond the limitation of the previous methods.
Technologies for Developing Predictive Atomistic and Coarse-Grained Force Fields for Ionic Liquid Property Prediction

DTIC Science & Technology

2008-07-29

minimization is performed. It is critical that all other force field parameters (for bonds, angles, charges, and Lennard-Jones interactions) be pre...and tailoring the parameterization accordingly may be critical . For Phase I, the above described procedure was performed manually to obtain dihedral... critical that a reliable approach is available to guide experimental efforts and design. In addition, the automation of force field development will
Ethyl 2-(4-chloro-2-oxo-2,3-dihydro-1,3-benzothiazol-3-yl)acetate

PubMed Central

Shen, Wen-Tong; Yao, Cheng

2009-01-01

In the molecule of the title compound, C11H10ClNO3S, the benzene and thiazole rings are oriented at a dihedral angle of 1.25 (3)°. Intramolecular C—H⋯O and C—H⋯Cl interactions result in the formation of two five-membered rings which both adopt envelope conformations. PMID:21582452
1-(4-Methyl-1-naphthyl)ethanone

PubMed Central

Hu, Yong-Hong; Zhao, Xiao-Lei; Yang, Wen-Ge; Yao, Jin-Feng; Lu, Xiu-Tao

2008-01-01

In the molecule of the title compound, C13H12O, the two aromatic rings are oriented at a dihedral angle of 2.90 (3)°. An intramolecular C—H⋯O hydrogen bond results in the formation of a non-planar six-membered ring, which adopts an envelope conformation. In the crystal structure, intermolecular C—H⋯O hydrogen bonds link the molecules. PMID:21581284
N-Benzylpyridin-2-amine

PubMed Central

Wang, Jun; Dai, Chuntao; Nie, Jianhua

2010-01-01

In the crystal of the title compound, C12H12N2, intermolecular N—H⋯N hydrogen bonds form rings of graph-set motif R 2 2(8) and C—H⋯π interactions further consolidate the dimers. Neighbouring dimers are further connected into a three-dimensional network by C—H⋯π interactions. The benzyl and pyridyl rings form a dihedral angle of 67.2 (1)° PMID:21589385
1-[1-(4-Chlorophenyl)ethylidene]carbonohydrazide

PubMed Central

Du, Lingyun; Du, Lei; Wang, Shuhao

2009-01-01

The molecular skeleton of the title molecule, C9H11ClN4O, is essentially planar, the dihedral angle between the ring and the and N/N/C plane being 6.7 (3)°. In the crystal, intermolecular N—H⋯O and N—H⋯N hydrogen bonds link the molecules into ribbons propagated along [010]. PMID:21577542
4-Meth-oxy-N-(1-methyl-1H-indazol-5-yl)benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Geffken, Detlef; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

The indazole ring system [maximum deviation = 0.013 (2) Å] of the title compound, C15H15N3O3S, makes a dihedral angle of 50.11 (7)° with the benzene ring. In the crystal, cohesion is provided by C-H⋯O and N-H⋯N hydrogen bonds, which link the molecules into chains propagating along the b-axis direction.
2-[(3-Propylsulfanyl-5-p-tolyl-4H-1,2,4-triazol-4-yl)iminomethyl]phenol

PubMed Central

Wang, Wei; Liu, Qing-lei; Xu, Chao; Wu, Wen-peng; Gao, Yan

2011-01-01

In the title molecule, C19H20N4OS, the two benzene rings form dihedral angles of 16.2 (1) and 12.0 (1)°, respectively, with the central triazole ring. In the crystal, intermolecular O—H⋯N hydrogen bonds link molecules into chains in the [010] direction. PMID:22058906
Exploring the origin of the internal rotational barrier for molecules with one rotatable dihedral angle

PubMed Central

Liu, Shubin; Govind, Niranjan; Pedersen, Lee G.

2008-01-01

Continuing our recent endeavor, we systematically investigate in this work the origin of internal rotational barriers for small molecules using the new energy partition scheme proposed recently by one of the authors [S. B. Liu, J. Chem. Phys. 126, 244103 (2007)], where the total electronic energy is decomposed into three independent components, steric, electrostatic, and fermionic quantum. Specifically, we focus in this work on six carbon, nitrogen, and oxygen containing hydrides, CH3CH3, CH3NH2, CH3OH, NH2NH2, NH2OH, and H2O2, with only one rotatable dihedral angle ∠H–X–Y–H (X,Y=C,N,O). The relative contributions of the different energy components to the total energy difference as a function of the internal dihedral rotation will be considered. Both optimized-geometry (adiabatic) and fixed-geometry (vertical) differences are examined, as are the results from the conventional energy partition and natural bond orbital analysis. A wealth of strong linear relationships among the total energy difference and energy component differences for different systems have been observed but no universal relationship applicable to all systems for both cases has been discovered, indicating that even for simple systems such as these, there exists no omnipresent, unique interpretation on the nature and origin of the internal rotation barrier. Different energy components can be employed for different systems in the rationalization of the barrier height. Confirming that the two differences, adiabatic and vertical, are disparate in nature, we find that for the vertical case there is a unique linear relationship applicable to all the six molecules between the total energy difference and the sum of the kinetic and electrostatic energy differences. For the adiabatic case, it is the total potential energy difference that has been found to correlate well with the total energy difference except for ethane whose rotation barrier is dominated by the quantum effect. PMID:19044862
Supra-molecular architecture in a co-crystal of the N(7)-H tautomeric form of N (6)-benzoyl-adenine with adipic acid (1/0.5).

PubMed

Swinton Darious, Robert; Thomas Muthiah, Packianathan; Perdih, Franc

2016-06-01

The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one mol-ecule of N (6)-benzoyl-adenine (BA) and one half-mol-ecule of adipic acid (AA), the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7)°. The N (6)-benzoyl-adenine mol-ecule crystallizes in the N(7)-H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intra-molecular N-H⋯O hydrogen bonding between the carbonyl (C=O) group and the N(7)-H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7) ring motif. The two carboxyl groups of adipic acid inter-act with the Watson-Crick face of the BA mol-ecules through O-H⋯N and N-H⋯O hydrogen bonds, generating an R 2 (2)(8) ring motif. The latter units are linked by N-H⋯N hydrogen bonds, forming layers parallel to (10-5). A weak C-H⋯O hydrogen bond is also present, linking adipic acid mol-ecules in neighbouring layers, enclosing R (2) 2(10) ring motifs and forming a three-dimensional structure. C=O⋯π and C-H⋯π inter-actions are also present in the structure.
SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints

NASA Astrophysics Data System (ADS)

Curtis, Joseph E.; Raghunandan, Sindhu; Nanda, Hirsh; Krueger, Susan

2012-02-01

A program to construct ensembles of biomolecular structures that are consistent with experimental scattering data are described. Specifically, we generate an ensemble of biomolecular structures by varying sets of backbone dihedral angles that are then filtered using experimentally determined restraints to rapidly determine structures that have scattering profiles that are consistent with scattering data. We discuss an application of these tools to predict a set of structures for the HIV-1 Gag protein, an intrinsically disordered protein, that are consistent with small-angle neutron scattering experimental data. We have assembled these algorithms into a program called SASSIE for structure generation, visualization, and analysis of intrinsically disordered proteins and other macromolecular ensembles using neutron and X-ray scattering restraints. Program summaryProgram title: SASSIE Catalogue identifier: AEKL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3 No. of lines in distributed program, including test data, etc.: 3 991 624 No. of bytes in distributed program, including test data, etc.: 826 Distribution format: tar.gz Programming language: Python, C/C++, Fortran Computer: PC/Mac Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.6.6) RAM: 1 GB Classification: 3 External routines: Python 2.6.5, numpy 1.4.0, swig 1.3.40, scipy 0.8.0, Gnuplot-py-1.8, Tcl 8.5, Tk 8.5, Mac installation requires aquaterm 1.0 (or X window system) and Xcode 3 development tools. Nature of problem: Open source software to generate structures of disordered biological molecules that subsequently allow for the comparison of computational and experimental results is limiting the use of scattering resources. Solution method: Starting with an all atom model of a protein, for example, users can input regions to vary dihedral angles, ensembles of structures can be generated. Additionally, simple two-body rigid-body rotations are supported with and without disordered regions. Generated structures can then be used to calculate small-angle scattering profiles which can then be filtered against experimentally determined data. Filtered structures can be visualized individually or as an ensemble using density plots. In the modular and expandable program framework the user can easily access our subroutines and structural coordinates can be easily obtained for study using other computational physics methods. Additional comments: The distribution file for this program is over 159 Mbytes and therefore is not delivered directly when download or Email is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Varies depending on application. Typically 10 minutes to 24 hours depending on the number of generated structures.
Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.

PubMed

Curuksu, Jeremy; Zacharias, Martin

2009-03-14

Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simulations performed at different temperatures (T-RexMD) can achieve improved conformational sampling. However, in the case of T-RexMD the computational demand grows rapidly with system size. A Hamiltonian RexMD method that specifically enhances coupled dihedral angle transitions has been developed. The method employs added biasing potentials as replica parameters that destabilize available dihedral substates and was applied to study coupled dihedral transitions in nucleic acid molecules. The biasing potentials can be either fixed at the beginning of the simulation or optimized during an equilibration phase. The method was extensively tested and compared to conventional MD simulations and T-RexMD simulations on an adenine dinucleotide system and on a DNA abasic site. The biasing potential RexMD method showed improved sampling of conformational substates compared to conventional MD simulations similar to T-RexMD simulations but at a fraction of the computational demand. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules.
An energy function for dynamics simulations of polypeptides in torsion angle space

NASA Astrophysics Data System (ADS)

Sartori, F.; Melchers, B.; Böttcher, H.; Knapp, E. W.

1998-05-01

Conventional simulation techniques to model the dynamics of proteins in atomic detail are restricted to short time scales. A simplified molecular description, in which high frequency motions with small amplitudes are ignored, can overcome this problem. In this protein model only the backbone dihedrals φ and ψ and the χi of the side chains serve as degrees of freedom. Bond angles and lengths are fixed at ideal geometry values provided by the standard molecular dynamics (MD) energy function CHARMM. In this work a Monte Carlo (MC) algorithm is used, whose elementary moves employ cooperative rotations in a small window of consecutive amide planes, leaving the polypeptide conformation outside of this window invariant. A single of these window MC moves generates local conformational changes only. But, the application of many such moves at different parts of the polypeptide backbone leads to global conformational changes. To account for the lack of flexibility in the protein model employed, the energy function used to evaluate conformational energies is split into sequentially neighbored and sequentially distant contributions. The sequentially neighbored part is represented by an effective (φ,ψ)-torsion potential. It is derived from MD simulations of a flexible model dipeptide using a conventional MD energy function. To avoid exaggeration of hydrogen bonding strengths, the electrostatic interactions involving hydrogen atoms are scaled down at short distances. With these adjustments of the energy function, the rigid polypeptide model exhibits the same equilibrium distributions as obtained by conventional MD simulation with a fully flexible molecular model. Also, the same temperature dependence of the stability and build-up of α helices of 18-alanine as found in MD simulations is observed using the adapted energy function for MC simulations. Analyses of transition frequencies demonstrate that also dynamical aspects of MD trajectories are faithfully reproduced. Finally, it is demonstrated that even for high temperature unfolded polypeptides the MC simulation is more efficient by a factor of 10 than conventional MD simulations.
A rare positively charged nicotinic acid disulfide: 2,2′-dithiodinicotinic acid hydrochloride monohydrate

PubMed Central

McGuire, Chad M.; Albrecht-Schmitt, Thomas E.

2018-01-01

The title compound {systematic name: 3-carboxy-2-[2-(3-carboxypyridin-2-yl)disulfan-1-yl)]pyridin-1-ium chloride monohydrate}, C12H9N2O4S2 +·Cl−·H2O, crystallizes in the triclinic space group P . A pair of 2-mercaptonicotinic acid moieties is connected by a 2,2′-disulfide bond with a dihedral angle of 78.79 (3)°. One of the N atom is protonated, as are both carboxylate groups, resulting in an overall +1 charge on the dimer. The structure comprises a zigzagging layer of the dimerized dithiodinicotinic acid rings, with charge-balancing chloride ions and water molecules between the layers. Hydrogen bonding between the chloride and water sites with the dimer appears to hold the structure together. Nearest neighbor nicotinic acid rings are offset when viewed down the a axis, suggesting no added stability from ring stacking. The asymmetric unit corresponds to the empirical formula of the compound, and it packs with two formula units per unit cell.
An accurate coarse-grained model for chitosan polysaccharides in aqueous solution.

PubMed

Tsereteli, Levan; Grafmüller, Andrea

2017-01-01

Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties.
An accurate coarse-grained model for chitosan polysaccharides in aqueous solution

PubMed Central

Tsereteli, Levan

2017-01-01

Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties. PMID:28732036
Force field dependent solution properties of glycine oligomers

PubMed Central

Drake, Justin A.

2015-01-01

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623
a 480 MHz Chirped-Pulse Fourier-Transform Microwave Spectrometer: Construction and Measurement of the Rotational Spectra of Divinyl Silane and 3,3-DIFLUOROPENTANE

NASA Astrophysics Data System (ADS)

Obenchain, Daniel A.; Steber, Amanda L.; Elliott, Ashley A.; Peebles, Rebecca A.; Peebles, Sean A.; Wurrey, Charles J.; Guirgis, Gamil A.

2010-06-01

A chirped-pulse Fourier-transform microwave (CP-FTMW) spectrometer based on the original Pate design has been constructed to allow analysis of any 480 MHz region in the 7 - 18 GHz range. A 1 μs chirped-pulse (0 - 240 MHz) from an arbitrary function generator is mixed with output from a microwave synthesizer and used to polarize a supersonic gas expansion; the resulting free induction decay is collected over 20 μs and Fourier-transformed on a 500 MHz oscilloscope to produce a rotational spectrum. A variety of molecules have now been studied with this instrument and results will be presented for numerous conformers of divinyl silane (predicted μtotal = 0.6 - 0.7 D) and the more polar 3,3-difluoropentane (predicted μtotal = 2.5 - 2.8 D). Two of the three possible conformers of divinyl silane were assigned (both having a C_1=C_2-Si-C_3 dihedral angle of -120° and a {C_2-Si-C_3=C_4} dihedral of either 0° (C_1 symmetry) or -120° (C_2 symmetry)). For 3,3-difluoropentane, three of the four possible {conformers} were identified: anti-gauche (C_1), gauche-gauche (C_2) and anti-anti (C2v). While rotational spectra for only the silicon isotopologues were observed for divinyl silane, measurement of the 13C spectra of 3,3-difluoropentane allowed heavy atom structure determinations for the anti-gauche and gauche-gauche conformers. Initial assignments of all spectra were made on the CP-FTMW {spectrometer}, and a Balle-Flygare FTMW spectrometer was used to compare frequencies of measured transitions and also to provide Stark effect data. Substitution (r_s) and inertial fit (r_0) structures will be compared with computational data and instrumental details will be presented. G.G. Brown, B.C. Dian, K.O. Douglass, S.M. Geyer, S.T. Shipman, B.H. Pate, Rev. Sci. Instrum., 79, (2008), 053103.
4,4′-[4,4′-Sulfonylbis(p-phenyleneoxy)]dibutanoic acid

PubMed Central

Fu, Chun-Yan; Liu, Yong-Hui; Zhou, Zhong-Liu; Tang, Hong

2011-01-01

In the title compound, C20H22O8S, the dihedral angle between the two benzene rings is 81.6 (3)°. The benzene-connected portions of the alkoxy substituents are almost coplanar with their respective rings [C—C—O—C torsion angles of 174.77 (17) and −178.5 (4)°]. One of the butanoic acid groups is disordered over two conformations with a site-occupancy ratio 0.719 (6):0.281 (6). In the crystal, pairs of O—H⋯O hydrogen bonds link the molecules into infinite zigzag chains along [130]. PMID:21754375
4-(5-Hydroxymethyl-2-methoxyphenoxy)benzoic acid

PubMed Central

Niu, Yanyan; Wu, Bo

2011-01-01

The title compound, C15H14O5, crystallizes with two independent molecules in the asymmetric unit in which the benzene rings are inclined at dihedral angles of 79.4 (1) and 84.2 (1)°. In the crystal, intermolecular O—H⋯O hydrogen bonds link the molecules into double chains propagating in [001]. PMID:21754394

N-(4,4′-Dibromo-[1,1′-biphenyl]-2-yl)benzamide

PubMed Central

Novina, J. Josephine; Vasuki, G.; Baheti, Abhishek; Thomas, K. R. Justin

2013-01-01

In the title compound, C19H13Br2NO, the dihedral angle between the rings of the biphenyl group is 53.59 (14)°. The ring of the benzamide group is inclined to the phenyl rings of the biphenyl group by 23.87 (15) and 75.89 (15)°. There are no significant intermolecular interactions in the crystal structure. PMID:23424503
3,3,6,6-Tetramethyl-9-(2-nitrophenyl)-3,4,6,7-tetrahydro-2H-xanthene-1,8(5H,9H)-dione

PubMed Central

Mo, Yingming; Zang, Hong-Jun; Cheng, Bo-Wen

2010-01-01

In the title compound, C23H25NO5, the pyran ring adopts a flattened boat conformation, while the two cyclohexenone rings are in envelope conformations. The 3-nitrophenyl ring is almost perpendicular to the pyran ring, making a dihedral angle of 87.1 (3)°. PMID:21588418
2-Ferrocenyl-3-methoxy-6-methylpyridine

PubMed Central

Xu, Chen; Hao, Xin-Qi; Liu, Fang; Wu, Xiu-Juan; Song, Mao-Ping

2009-01-01

In the title compound, [Fe(C5H5)(C12H12NO)], the dihedral angle between the pyridyl and substituted cyclopentadienyl rings is 23.58 (3)°. The crystal structure is characterized by weak intermolecular C—H⋯N hydrogen-bonding contacts, leading to the formation of chains running parallel to the n-glide planes. A weak intermolecular C—H⋯π contact is also present. PMID:21583761
3-(4-Chlorophenyl)-7-methyl-4-(4-methylphenyl)-1-oxa-2,7-diazaspiro[4.5]dec-2-en-10-one

PubMed Central

Gayathri, D.; Velmurugan, D.; Ranjith Kumar, R.; Perumal, S.; Ravikumar, K.

2008-01-01

In the title compound, C21H21ClN2O2, the dihydroisoxazole ring adopts an envelope conformation and the piperidinone ring is in a chair conformation. The dihedral angle between the two benzene rings is 84.2 (1)°. The crystal used was an inversion twin. PMID:21201426
DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, S.-W., E-mail: sunsw0819@163.com; Zhang, X., E-mail: zhangx@hit.edu.cn; Wang, G.-F.

A series of 2-arylidenebenzocycloalkanones containing heterocyclic rings 1–8 were prepared and characterized by IR, {sup 1}H NMR and elemental analyses. X-ray diffraction study of 6 reveals that the cyclohexyl ring of the 3,4-dihydronaphthalen-1(2H)-one adopts a chair conformation with a maximum deviation of 0.547(3) Å and makes dihedral angles of 52.24(17)° and 11.23(16)°, respectively, with the benzene plane and the mean plane of the benzimidazole ring.
4-Methoxy-N-(1-methyl-1H-indazol-5-yl)benzenesulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Geffken, Detlef; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

The indazole ring system [maximum deviation = 0.013 (2) Å] of the title compound, C15H15N3O3S, makes a dihedral angle of 50.11 (7)° with the benzene ring. In the crystal, cohesion is provided by C—H⋯O and N—H⋯N hydrogen bonds, which link the molecules into chains propagating along the b-axis direction. PMID:24427037
Method of calculating retroreflector-array transfer functions. [laser range finders

NASA Technical Reports Server (NTRS)

Arnold, D. A.

1978-01-01

Techniques and equations used in calculating the transfer functions to relate the observed return laser pulses to the center of mass of the Lageos satellite retroflector array, and for most of the retroreflector-equipped satellites now in orbit are described. The methods derived include the effects of coherent interference, diffraction, polarization, and dihedral-angle offsets. Particular emphasis is given to deriving expressions for the diffraction pattern and active reflecting area of various cube-corner designs.
Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

DTIC Science & Technology

2009-01-01

implicit solvents on peptide structure and dynamics , we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two...end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those...to maintain the temperature of the systems. Introduction Molecular dynamics (MD) simulation techniques are widely used to study structure and
(2E)-3-(6-methoxynaphthalen-2-yl)-1-(pyridin-3-yl)prop-2-en-1-one and its cyclocondensation product with guanidine, (4RS)-2-amino-4-(6-methoxynaphthalen-2-yl)-6-(pyridin-3-yl)-3,4-dihydropyrimidine monohydrate: two types of hydrogen-bonded sheet.

PubMed

Nayak, Prakash S; Narayana, Badiadka; Yathirajan, Hemmige S; Hosten, Eric C; Betz, Richard; Glidewell, Christopher

2014-11-01

The structures of a chalcone and of its cyclocondensation product with guanidine are reported. In (2E)-3-(6-methoxynaphthalen-2-yl)-1-(pyridin-3-yl)prop-2-en-1-one, C19H15NO2, (I), the planes of the pyridine and naphthalene units make dihedral angles with that of the central spacer unit of 23.61 (13) and 23.57 (15)°, respectively, and a dihedral angle of 47.24 (9)° with each other. The molecules of (I) are linked into sheets by a combination of C-H···O and C-H···π(arene) hydrogen bonds. In the cyclocondensation product (4RS)-2-amino-4-(6-methoxynaphthalen-2-yl)-6-(pyridin-3-yl)-3,4-dihydropyrimidine monohydrate, C20H18N4O·H2O, (II), the dihydropyrimidine ring adopts a conformation best described as a shallow boat. The molecular components are linked by two N-H···O hydrogen bonds, two O-H···N hydrogen bonds and one N-H···N hydrogen bond to form complex sheets, with the methoxynaphthalene interdigitated between inversion-related pairs of sheets.
Steric interactions determine side-chain conformations in protein cores.

PubMed

Caballero, D; Virrueta, A; O'Hern, C S; Regan, L

2016-09-01

We investigate the role of steric interactions in defining side-chain conformations in protein cores. Previously, we explored the strengths and limitations of hard-sphere dipeptide models in defining sterically allowed side-chain conformations and recapitulating key features of the side-chain dihedral angle distributions observed in high-resolution protein structures. Here, we show that modeling residues in the context of a particular protein environment, with both intra- and inter-residue steric interactions, is sufficient to specify which of the allowed side-chain conformations is adopted. This model predicts 97% of the side-chain conformations of Leu, Ile, Val, Phe, Tyr, Trp and Thr core residues to within 20°. Although the hard-sphere dipeptide model predicts the observed side-chain dihedral angle distributions for both Thr and Ser, the model including the protein environment predicts side-chain conformations to within 20° for only 60% of core Ser residues. Thus, this approach can identify the amino acids for which hard-sphere interactions alone are sufficient and those for which additional interactions are necessary to accurately predict side-chain conformations in protein cores. We also show that our approach can predict alternate side-chain conformations of core residues, which are supported by the observed electron density. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
The thickness of the crystal mush on the floor of the Bushveld magma chamber

NASA Astrophysics Data System (ADS)

Holness, Marian B.; Cawthorn, R. Grant; Roberts, James

2017-12-01

The thickness of the crystal mush on magma chamber floors can be constrained using the offset between the step-change in the median value of dihedral angles formed at the junctions between two grains of plagioclase and a grain of another phase (typically clinopyroxene, but also orthopyroxene and olivine) and the first appearance or disappearance of the liquidus phase associated with the step-change in median dihedral angle. We determined the mush thickness in the Rustenburg Layered Suite of the Bushveld Complex at clinopyroxene-in (in Lower Main Zone) and magnetite-in (in Upper Zone). We also examined an intermittent appearance of cumulus apatite in Upper Zone, using both the appearance and disappearance of cumulus apatite. In all cases, the mush thickness does not exceed 4 m. These values are consistent with field observations of a mechanically rigid mush at the bases of both magnetitite and chromitite layers overlying anorthosite. Mush thickness of the order of a few metres suggests that neither gravitationally-driven compaction nor compositional convection within the mush layer is likely to have been important processes during solidification: adcumulates in the Bushveld are most likely to have formed at the top of the mush during primary crystallisation. Similarly, it is unlikely either that migration of reactive liquids occurs through large stretches of stratigraphy, or that layering is formed by mechanisms other than primary accumulation.
Crystal structures of 4-meth-oxy-N-(4-methyl-phenyl)benzene-sulfonamide and N-(4-fluoro-phenyl)-4-meth-oxy-benzene-sulfonamide.

PubMed

Rodrigues, Vinola Z; Preema, C P; Naveen, S; Lokanath, N K; Suchetan, P A

2015-11-01

Crystal structures of two N-(ar-yl)aryl-sulfonamides, namely, 4-meth-oxy-N-(4-methyl-phen-yl)benzene-sulfonamide, C14H15NO3S, (I), and N-(4-fluoro-phen-yl)-4-meth-oxy-benzene-sulfonamide, C13H12FNO3S, (II), were determined and analyzed. In (I), the benzene-sulfonamide ring is disordered over two orientations, in a 0.516 (7):0.484 (7) ratio, which are inclined to each other at 28.0 (1)°. In (I), the major component of the sulfonyl benzene ring and the aniline ring form a dihedral angle of 63.36 (19)°, while in (II), the planes of the two benzene rings form a dihedral angle of 44.26 (13)°. In the crystal structure of (I), N-H⋯O hydrogen bonds form infinite C(4) chains extended in [010], and inter-molecular C-H⋯πar-yl inter-actions link these chains into layers parallel to the ab plane. The crystal structure of (II) features N-H⋯O hydrogen bonds forming infinite one dimensional C(4) chains along [001]. Further, a pair of C-H⋯O inter-molecular inter-actions consolidate the crystal packing of (II) into a three-dimensional supra-molecular architecture.
COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.

PubMed

Andrews, Casey T; Elcock, Adrian H

2014-11-11

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions-which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)-quantitatively reproduced all of the "target" MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic ( PLoS Comput. Biol. 2014 , 5 , e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP's nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins.
COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

PubMed Central

2015-01-01

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins. PMID:25400526
Polarimetric subspace target detector for SAR data based on the Huynen dihedral model

NASA Astrophysics Data System (ADS)

Larson, Victor J.; Novak, Leslie M.

1995-06-01

Two new polarimetric subspace target detectors are developed based on a dihedral signal model for bright peaks within a spatially extended target signature. The first is a coherent dihedral target detector based on the exact Huynen model for a dihedral. The second is a noncoherent dihedral target detector based on the Huynen model with an extra unknown phase term. Expressions for these polarimetric subspace target detectors are developed for both additive Gaussian clutter and more general additive spherically invariant random vector clutter including the K-distribution. For the case of Gaussian clutter with unknown clutter parameters, constant false alarm rate implementations of these polarimetric subspace target detectors are developed. The performance of these dihedral detectors is demonstrated with real millimeter-wave fully polarimetric SAR data. The coherent dihedral detector which is developed with a more accurate description of a dihedral offers no performance advantage over the noncoherent dihedral detector which is computationally more attractive. The dihedral detectors do a better job of separating a set of tactical military targets from natural clutter compared to a detector that assumes no knowledge about the polarimetric structure of the target signal.
Molecular structure, FT IR, NMR, UV, NBO and HOMO-LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311++G(d,2p) basis sets.

PubMed

Khajehzadeh, Mostafa; Moghadam, Majid

2017-06-05

Structural and molecular properties of antidepressants 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile were examined using quantum mechanics of Density Functional Theory (DFT)/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets to study the therapeutic properties of the drug. For this, the structure of desired material was optimized by the computer calculation method and with the use of powerful Gaussian 09 software. Then the lowest energy value and the bond length, bond angle and dihedral angle between its constituent atoms in the crystal structure of the desired material were measured from the optimized values. Then the amount of positive and negative charges, polarizability and dipole moment of its atoms using Mulliken charge and Natural atomic charges, DFT/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets were determined and the results were compared with each other for individual atoms and by mentioned methods. Also the type of stretching vibrations and bending vibrations between the constituent atoms of the molecule were specified using mentioned computational methods and FT IR vibrational spectra. The experimental spectrum of this material was taken to determine the functional groups and the computational and experimental values were compared to each other and Nuclear Magnetic Resonance (NMR) was used to specify the isomer shift between the carbons and protons in the presence of polar and nonpolar solvents. Also Natural Bond Orbital (NBO) was used to determine the type of electron transfers in σ→σ∗ and π→π∗ and LP(1)→σ∗ and LP(2)→σ∗ and the amount of hardness and softness in molecule was determined using the difference between ionization energy and electron affinity energy in constituent atoms of that molecule in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and in the presence of solvents H 2 O, CH 3 CN and C 6 H 12 . UV-Vis spectrum of the drug was taken using DFT/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets as well as solvents H 2 O, CH 3 CN and C 6 H 12 and the associated transmissions were examined. Copyright © 2017 Elsevier B.V. All rights reserved.
All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

PubMed

Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

2015-05-12

We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N -acetylglucosamine, N -acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from the extensive analysis of conformational properties of glycoprotein structures reported in the Protein Data Bank. Use of the BPMC search leads to significant improvements in sampling efficiency for glycan simulations. Moreover, good agreement with the X-ray glycoprotein structures is achieved for all glycan chain lengths. Thus, average/median RMSDs are 0.81/0.68 Å for one-residue glycans and 1.32/1.47 Å for three-residue glycans. RMSD from the native structure for the lowest-energy conformation of the 12-residue glycan chain (PDB ID 3og2) is 1.53 Å. Additionally, results obtained for free short oligosaccharides using the new force field are in line with the available experimental data, i.e., the most populated conformations in solution are predicted to be the lowest energy ones. The newly developed parameters allow for the accurate modeling of linear and branched hexopyranose glycosides in heterogeneous systems.
Motion of a liquid bridge between nonparallel surfaces.

PubMed

Ataei, Mohammadmehdi; Tang, Tian; Amirfazli, Alidad

2017-04-15

Bulk motion of a liquid bridge between two nonparallel identical solid surfaces undergoing multiple loading cycles (compressing and stretching) was investigated numerically and experimentally. The effects of the following governing parameters were studied: the dihedral angle between the two surfaces (ψ), the amount of compressing and stretching (Δh), and wettability parameters i.e. the advancing contact angle (θ a ) and Contact Angle Hysteresis (CAH). Experiments were done using various combinations of ψ, Δh and on surfaces with different wettabilities to understand the effect of each parameter individually. Additionally, a numerical model using Surface Evolver software was developed to augment the experimental data and extract information about the shape of the bridge. An empirical function was proposed and validated to calculate the minimum amount of Δh needed to initiate the bulk motion (i.e. to overcome the initial lag of the motion in response to the compressing of the bridge), at a given dihedral angle ψ. The effect of governing parameters on magnitude and precision of the motion was investigated. The magnitude of the motion was found to be increased by increasing ψ and Δh, and/or by decreasing θ a and CAH. We demonstrated the possibility of modulating the precision of the motion with θ a . Additionally, it was shown that the magnitude of the motion (in one loading cycle) increases after each loading cycle, if the contact lines depin only on the narrower side of the bridge during compressing and only on the wider side during stretching (asymmetric depinning). Whereas, depinning on both sides of the bridge (symmetric depinning) reduced the magnitude of bridge motion in each cycle under cyclic loading. A larger ψ was found to convert symmetric depinning into asymmetric depinning. These findings not only enhance the understanding of bridge motion between nonparallel surfaces, but also are beneficial in controlling magnitude, precision, and lag of the motion in practical applications. Copyright © 2016 Elsevier Inc. All rights reserved.
Synthesis and Crystal Structure of a Chalcone Derivative

NASA Astrophysics Data System (ADS)

Singh, Vikram D.; Salian, Vinutha V.; Narayana, B.; Sarojini, B. K.; Kamni; Anthal, Sumati; Kant, Rajni

2017-12-01

(2E)-3-(anthrance-9-yl)-1-(3,4-dichlorophenyl)prop-2-en-1-one [C23H14OCl2] is synthesized and its crystal structure is determined by single X-ray diffraction. There exist two molecules in the asymmetric unit. The dihedral angle between the benzene and anthracene moiety of the molecule A and B is 86.51(12)° and 76.42(13)°, respectively. No classical hydrogen bonds are observed and only van der Waals forces stabilize the crystal packing.
3,6-Dimethyl-N 1,N 4-bis(1-phenylethyl)-1,4-dihydro-1,2,4,5-tetrazine-1,4-dicarboxamide

PubMed Central

Rao, Guo-Wu; Li, Qi; Lu, Xiao-Jing

2012-01-01

In the title molecule, C22H26N6O2, the central tetrazine ring exhibits a boat conformation, and the two phenyl rings form a dihedral angle of 88.39 (6)°. In the crystal, weak N—H⋯O and C—H⋯O hydrogen bonds link molecules into layers parallel to the ab plane. PMID:22347041

2-[(2-Hydroxy-4-methoxybenzylidene)azaniumyl]benzoate monohydrate

PubMed Central

Hang, Zhi-Xi; Dong, Bo; Wang, Xing-Wen

2010-01-01

In the title compound, C15H13NO4·H2O, the Schiff base exists in a zwitterionic form and a bifurcated intramolecular N—H⋯(O,O) hydrogen bond generates two S(6) rings. The dihedral angle between the two benzene rings is 25.8 (2)°. The crystal structure is stabilized by intermolecular O—H⋯O hydrogen bonds. PMID:21587989
N′-[(E)-4-Hydroxy-3-methoxybenzylidene]pyridine-4-carbohydrazide

PubMed Central

Shafiq, Zahid; Yaqub, Muhammad; Tahir, M. Nawaz; Hussain, Abid; Iqbal, M. Saeed

2009-01-01

In the title compound, C14H13N3O3, the two six-membered rings are oriented at a dihedral angle of 15.17 (11)° and an intramolecular O—H⋯O hydrogen bond occurs. In the crystal, molecules interact by way of N—H⋯O, O—H⋯N and C—H⋯O hydrogen bonds, thereby generating S(5) chain and R 2 1(7) ring motifs. PMID:21578481
(Z)-5-(4-Fluorobenzylidene)-1,3-thiazolidine-2,4-dione

PubMed Central

Sun, Hong-Shun; Xu, Ye-Ming; He, Wei; Tang, Shi-Gui; Guo, Cheng

2008-01-01

In the title compound, C10H6FNO2S, the benzene and thiazolidine rings make a dihedral angle of 7.52 (3)°. Intramolecular C—H⋯O and C—H⋯S hydrogen bonds result in the formation of nearly planar five- and six-membered rings; the adjacent rings are nearly coplanar. In the crystal structure, intermolecular N—H⋯O hydrogen bonds link the molecules. PMID:21201543
4-Nitrobenzyl 2-bromoacetate

PubMed Central

Zhu, Kai; Liu, Hui; Wang, Yan-Hua; Han, Ping-Fang; Wei, Ping

2009-01-01

In the molecule of the title compound, C9H8BrNO4, the acetate group is close to planar [maximum deviation = 0.042 (3) Å] and is oriented at a dihedral angle of 73.24 (3)° with respect to the aromatic ring. In the crystal structure, intermolecular C—H⋯O interactions link the molecules into a three-dimensional network, forming R 2 2(10) ring motifs. PMID:21582813
2,2',5,5'-Tetra-methyl-1,1'-(hexane-1,6-di-yl)di-1H-pyrrole.

PubMed

Santos, Ana C; Ramos Silva, Manuela; Monsanto, Paula V; Matos Beja, Ana; Sobral, Abilio J F N

2009-06-17

The mol-ecule of the title compound, C(18)H(28)N(2), composed of two 2,5-dimethyl-pyrrole groups linked by a hexane chain, lies across a crystallographic inversion centre. The mean plane of the pyrrole ring is almost perpendicular to the mean plane of the central chain, making a dihedral angle of 89.09 (8)°. The crystal structure is stabilized by inter-molecular C-H⋯π inter-actions.
(E)-3-Methyl-2,6-diphenylpiperidin-4-one O-(3-methylbenzoyl)oxime

PubMed Central

Kathiravan, V.; Krishnan, K. Gokula; Mohandas, T.; Thanikachalam, V.; Sakthivel, P.

2014-01-01

In the title compound, C26H26N2O2, the piperidine ring exhibits a chair conformation. The phenyl rings are attached to the central heterocycle in an equatorial position. The dihedral angle between the planes of the phenyl rings is 57.58 (8)°. In the crystal, C—H⋯O interactions connect the molecules into zigzag chains along [001]. PMID:25249925
4-Substituted-2-Methoxyphenol: Suitable Building Block to Prepare New Bioactive Natural-like Hydroxylated Biphenyls.

PubMed

Dettori, Maria Antonietta; Fabbri, Davide; Pisano, Marina; Rozzo, Carla; Palmieri, Giuseppe; Dess, Alessandro; Dallocchio, Roberto; Delogu, Giovanna

2015-02-01

A small collection of eugenol- and curcumin-analog hydroxylated biphenyls was prepared by straightforward methods starting from natural 4-substituted-2-methoxyphenols and their antitumoral activity was evaluated in vitro . Two curcumin-biphenyl derivatives showed interesting growth inhibitory activities on different malignant melanoma cell lines with IC 50 ranging from 13 to 1 µM. Preliminary molecular modeling studies were carried out to evaluate conformations and dihedral angles suitable for antiproliferative activity in hydroxylated biphenyls bearing a side aliphatic chain.
New assessment of a structural alphabet

PubMed Central

de Brevern, Alexandre G.

2005-01-01

Summary A statistical analysis of the Protein Databank (PDB) structures had led us to define a set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one defined by the (Φ, Ψ) dihedral angles of 5 consecutive residues. Here, we analyze the effect of the enlargement of the PDB on the PBs’ definition. The results highlight the quality of the 3D approximation ensured by the PBs. These last could be of great interest in ab initio modeling. PMID:15996119
N-(1H-Indazol-5-yl)-4-meth-oxy-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Saadi, Mohamed; El Ammari, Lahcen

2013-10-26

In the title compound, C14H13N3O3S, the fused ring system is almost planar, the largest deviation from the mean plane being 0.023 (2) Å, and makes a dihedral angle of 47.92 (10)° with the benzene ring of the benzene-sulfonamide moiety. In the crystal, mol-ecules are connected through N-H⋯O hydrogen bonds and weak C-H⋯O contacts, forming a two-dimensional network which is parallel to (010).
Nominal SARAL Transfer Function

NASA Technical Reports Server (NTRS)

Arnold, David A.; Lemoine, Frank (Editor)

2015-01-01

This paper gives a calculation of the range correction and cross section of the SARAL (Satellite with Argos and ALtiKa) Indian/French ocean radar satellite retroreflector array assuming the cube corners are coated and have a dihedral angle offset of about 1.5 arcseconds to account for velocity aberration. The cubes are assumed to all have the same orientation within the mounting. The derived range correction may be applied in precise orbit determination analyses that use Satellite Laser Ranging (SLR) data to SARAL.
Picric acid-2,4,6-trichloro-aniline (1/1).

PubMed

Wang, Wan-Qiang

2011-04-01

In the title adduct, C(6)H(4)Cl(3)N·C(6)H(3)N(3)O(7), the two benzene rings are almost coplanar, with a dihedral angle of 1.19 (1)° and an inter-ring centroid-centroid separation of 4.816 (2) Å. The crystal structure is stabilized by inter-molecular N-H⋯O(nitro) hydrogen bonds, giving a chain structure. In addition, there are phenol-nitro O-H⋯O inter-actions.
N-(Adamantan-1-yl)-1,2,3,4-tetra-hydro-iso-quinoline-2-carbo-thio-amide.

PubMed

El-Emam, Ali A; Al-Abdullah, Ebtehal S; Al-Tuwaijri, Hanaa M; Chidan Kumar, C S; Fun, Hoong-Kun

2013-11-23

In the title compound, C20H26N2S, the N-containing six-membered ring adopts a boat conformation and the dihedral angle between the thio-carbamide group and the benzene ring is 49.67 (9)°. An intra-molecular C-H⋯S hydrogen bond generates an S(6) ring motif. The N-H group is sterically hindered and there are no significant inter-molecular inter-actions beyond van der Waals contacts.
3-(2,4-Dichloroanilino)isobenzofuran-1(3H)-one1

PubMed Central

Odabaşoğlu, Mustafa; Büyükgüngör, Orhan

2008-01-01

In the molecule of the title compound, C14H9Cl2NO2, the essentially planar phthalide group is oriented at a dihedral angle of 63.23 (5)° with respect to the substituted aromatic ring. In the crystal structure, intermolecular C—H⋯O and N—H⋯O hydrogen bonds link the molecules, generating R 4 4(21) ring motifs to form a three-dimensional network. PMID:21202144
A Wind-Tunnel Investigation of a Transonic-Transport Configuration Utilizing Drag-Reducing Devices at Mach Numbers from 0.20 to 1.03

NASA Technical Reports Server (NTRS)

Loving, Donald L.

1961-01-01

The static longitudinal stability and control and lateral characteristics of a transonic-transport model, incorporating recent drag-reducing devices, has been investigated in the Langley 8-foot transonic pressure tunnel. The wing was cambered, had a thickened root and a taper ratio of 0.3. Wing sweepback angles of 45 degrees and 40 degrees were investigated with corresponding aspect ratios of 7 and 8, respectively. Modifications to the model for reducing the drag were: a forward fuselage addition and special bodies (four big enough to house jet engines) added to the upper surface of the wing. Other components and changes investigated included an empennage, a wing-tip body, wing fences, wing trailing-edge flaps, horizontal-tail settings, and wing dihedral angle. The investigation covered the Mach number range from 0.20 to 1.03 for the angle-of-attack range from -5 degrees to 15.4 degrees, and a sideslip angle of -5 degrees, in the Reynolds number range from 0.52 times 10(exp 6) to 1.94 times 10(exp 6) based on the wing mean aerodynamic chord. The various fuselage and wing additions delayed the drag-rise Mach number and greatly reduced the drag beyond the drag rise. The wing bodies markedly alleviated unstable pitch tendencies throughout the test Mach number range. At low landing speeds, the wing bodies exhibited little interference with the ability of trailing-edge flaps to increase the lift near maximum lift coefficient; and the use of fences greatly reduced the severe longitudinal instability trend at landing attitudes. The model with a 6 degree dihedral angle exhibited positive lateral and directional stability characteristics in the presence of the fuselage and wing additions. An increase in drag-rise Mach number associated with the fuselage and wing additions on the 40 degree sweptback wing combination was similar to that for the comparable 45 degree combination. These additions did, however, reduce the drag of the 40 degree sweptback configurations more than the 45 degree configurations in the transonic speed range.
(E)-1-(Pyridin-2-yl)-3-(3,4,5-trimethoxyphenyl)prop-2-en-1-one

PubMed Central

Fun, Hoong-Kun; Suwunwong, Thitipone; Chantrapromma, Suchada

2011-01-01

In the title heteroaryl chalcone derivative, C17H17NO4, the dihedral angle between the pyridine and benzene rings is 10.82 (5)°. The two methoxy groups at the meta positions are essentially coplanar with the attached benzene rings [C—O—C—C torsion angles = −0.97 (14) and 179.47 (9)°], whereas the methoxy group at the para position is twisted from the attached ring with a C—O—C—C torsion angle of −104.48 (11)°. A C—H⋯O close contact involving two of the methoxy groups generates an S(6) ring motif. In the crystal, molecules are linked by weak C—H⋯O interactions into columns along the b axis. PMID:22058997
Main types of optical beams giving predominant contributions to the light backscatter for the irregular hexagonal columns

NASA Astrophysics Data System (ADS)

Shishko, Victor A.; Konoshonkin, Alexander V.; Kustova, Natalia V.; Borovoi, Anatoli G.

2017-11-01

This work presents the estimation of contribution of the main types of optical beams to the light backscatter for randomly oriented hexagonal ice column, the right dihedral angle of which was distorted within the range of 0° (regular particle) to 10°. Calculations were obtained within the physical optics approximation. The wavelength was 532 nm and the refractive index was 1.3116. The results showed that the total contribution of the main types of optical beams to the total backscattering cross section reach the value of 85% at small distortion angle of the hexagonal column and at substantial distortion angle the total contribution of the main types of optical beams decrease up to 55% of the total backscattering cross section. The obtained conclusions can significantly reduce the calculation time in the case when there is no need for high accuracy of the calculation.
Dibenzo-18-crown-6–picric acid–water (1/2/3)

PubMed Central

Saleh, Muhammad Idiris; Kusrini, Eny; Rosli, Mohd Mustaqim; Fun, Hoong-Kun

2008-01-01

In the crown ether ring of the title compound, C20H24O6·2C6H3N3O7·3H2O, the O—C(H2)—C(H2)—O torsion angles indicate a gauche conformation of the ethyleneoxy units, while the C—O—C—C torsion angles indicate planarity of these segments; the dihedral angle between the two benzene rings is 44.53 (13)°. In both picric acid molecules, one of the nitro groups is twisted away from the attached ring. The molecules are linked into chains along the b axis via intermolecular O—H⋯O hydrogen bonds. In addition, the crystal structure is stabilized by C—H⋯O hydrogen bonds and π–π interactions [centroid–centroid distance between benzene rings = 3.5697 (16) Å]. PMID:21202944
Low-speed static and dynamic force tests of a generic supersonic cruise fighter configuration

NASA Technical Reports Server (NTRS)

Hahne, David E.

1989-01-01

Static and dynamic force tests of a generic fighter configuration designed for sustained supersonic flight were conducted in the Langley 30- by 60-foot tunnel. The baseline configuration had a 65 deg arrow wing, twin wing mounted vertical tails and a canard. Results showed that control was available up to C sub L,max (maximum lift coefficient) from aerodynamic controls about all axes but control in the pitch and yaw axes decreased rapidly in the post-stall angle-of-attack region. The baseline configuration showed stable lateral-directional characteristics at low angles of attack but directional stability occurred near alpha = 25 deg as the wing shielded the vertical tails. The configuration showed positive effective dihedral throughout the test angle-of-attack range. Forced oscillation tests indicated that the baseline configuration had stable damping characteristics about the lateral-directional axes.
3D visualization of molecular structures in the MOGADOC database

NASA Astrophysics Data System (ADS)

Vogt, Natalja; Popov, Evgeny; Rudert, Rainer; Kramer, Rüdiger; Vogt, Jürgen

2010-08-01

The MOGADOC database (Molecular Gas-Phase Documentation) is a powerful tool to retrieve information about compounds which have been studied in the gas-phase by electron diffraction, microwave spectroscopy and molecular radio astronomy. Presently the database contains over 34,500 bibliographic references (from the beginning of each method) for about 10,000 inorganic, organic and organometallic compounds and structural data (bond lengths, bond angles, dihedral angles, etc.) for about 7800 compounds. Most of the implemented molecular structures are given in a three-dimensional (3D) presentation. To create or edit and visualize the 3D images of molecules, new tools (special editor and Java-based 3D applet) were developed. Molecular structures in internal coordinates were converted to those in Cartesian coordinates.
2-({4-[4-(1H-Benzimidazol-2-yl)phenyl]-1H-1,2,3-triazol-1-yl}methoxy)ethanol

PubMed Central

Ouahrouch, Abdelaaziz; Taourirte, Moha; Lazrek, Hassan B.; Bats, Jan W.; Engels, Joachim W.

2012-01-01

In the title molecule, C18H17N5O2, the dihedral angle between the benzene plane and the benzimidazole plane is 19.8 (1)° and the angle between the benzene plane and the triazole plane is 16.7 (1)°. In the crystal, molecules are connected by O—H⋯N hydrogen bonds, forming zigzag chains along the c-axis direction. The chains are connected by bifurcated N—H⋯(N,N) hydrogen bonds into layers parallel to (100). These layers are connected along the a-axis direction by weak C—H⋯O contacts, forming a three-dimensional network. PMID:22719663

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