scholarly journals On the influence of small chemical changes upon the supramolecular association in substituted 2-(phenoxy)-1,4-naphthoquinones

2019 ◽  
Vol 234 (3) ◽  
pp. 183-200
Author(s):  
Marlon D.L. Tonin ◽  
Simon J. Garden ◽  
Mukesh M. Jotani ◽  
James L. Wardell ◽  
Edward R.T. Tiekink
Keyword(s):  
Three Dimensional ◽  
Ring System ◽  
Molecular Packing ◽  
Three Dimensions ◽  
Π Interactions ◽  
X Ray Crystallography ◽  
The Common ◽  
Layer Region ◽  
Small Chemical

Abstract X-ray crystallography reveals the common feature of the title compounds is a 1,4-naphthoquinone ring system with a substituted phenoxy residue adjacent to an oxo-group to give 1 (H), 2 (3-Br), 3 (3-CF3), 4 (4-CN) and 5 (4-NO2). To a first approximation the fused ring system along with the two oxo substituents is planar with the major difference between the molecules relating to the relative orientations of the pendant phenoxy residues: dihedral angles range from 56.56(4)° (3) to 87.52(10)° (2). The presence of intermolecular C–H···O interactions is the common feature of the supramolecular association in the crystals of 1–5. In each of 1 and 5, these extend in three-dimensions but, only to supramolecular dimers in 4, chains in 2 and layers in 3. Each crystal also features C=O···π interactions, pointing to the importance of these points of contact in this series di-oxocompounds. In 2, these, along with C–Br···π interactions lead to a three-dimensional architecture. For 3, the C=O···π and π···π interactions occur within the layers which stack without directional interactions between them. In 4, C–H···O and C=O···π interactions combine to give a supramolecular layer, which also stack without directional interactions in the inter-layer region. Further analysis of the molecular packing was conducted by a Hirshfeld surface analysis (HSA). This points to the significant role of H···H, C···H/H···C and O···H/H···O contacts in the packing of 1. Notably different roles for these contacts are found in the other crystals correlating with the participation of the respective substituents in the molecular packing. The HSA suggests the association between layers in 3 (weak F···F and H···F interactions) and 4 (weak H···N interactions) is contributed by the phenoxy-substituents.

scholarly journals Development and assessment of CootVR, a virtual reality computer program for model building

2021 ◽  
Vol 77 (1) ◽  
pp. 19-27
Author(s):  
Hamish Todd ◽  
Paul Emsley
Keyword(s):  
Virtual Reality ◽  
Computer Program ◽  
Model Building ◽  
Three Dimensional ◽  
Specific Model ◽  
Three Dimensions ◽  
Biological Macromolecules ◽  
Data Set ◽  
X Ray Crystallography ◽  
Order Of Magnitude

Biological macromolecules have complex three-dimensional shapes that are experimentally examined using X-ray crystallography and electron cryo-microscopy. Interpreting the data that these methods yield involves building 3D atomic models. With almost every data set, some portion of the time put into creating these models must be spent manually modifying the model in order to make it consistent with the data; this is difficult and time-consuming, in part because the data are `blurry' in three dimensions. This paper describes the design and assessment of CootVR (available at http://hamishtodd1.github.io/cvr), a prototype computer program for performing this task in virtual reality, allowing structural biologists to build molecular models into cryo-EM and crystallographic data using their hands. CootVR was timed against Coot for a very specific model-building task, and was found to give an order-of-magnitude speedup for this task. A from-scratch model build using CootVR was also attempted; from this experience it is concluded that currently CootVR does not give a speedup over Coot overall.

Bringing Dynamic Geometry to Three Dimensions

2015 ◽  
pp. 68-99
Author(s):  
Nicholas H. Wasserman
Keyword(s):  
Teaching And Learning ◽  
Spatial Reasoning ◽  
Mathematics Classroom ◽  
Three Dimensional ◽  
Dynamic Geometry ◽  
State Standards ◽  
Three Dimensions ◽  
Two Dimensional ◽  
The Common ◽  
K 12

Contemporary technologies have impacted the teaching and learning of mathematics in significant ways, particularly through the incorporation of dynamic software and applets. Interactive geometry software such as Geometers Sketchpad (GSP) and GeoGebra has transformed students' ability to interact with the geometry of plane figures, helping visualize and verify conjectures. Similar to what GSP and GeoGebra have done for two-dimensional geometry in mathematics education, SketchUp™ has the potential to do for aspects of three-dimensional geometry. This chapter provides example cases, aligned with the Common Core State Standards in mathematics, for how the dynamic and unique features of SketchUp™ can be integrated into the K-12 mathematics classroom to support and aid students' spatial reasoning and knowledge of three-dimensional figures.

Boundary layer over a blunt body at low incidence with circumferential reversed flow

1975 ◽  
Vol 72 (1) ◽  
pp. 49-65 ◽  
Author(s):  
K. C. Wang
Keyword(s):  
Boundary Layer ◽  
Skin Friction ◽  
Blunt Body ◽  
Three Dimensional ◽  
Prolate Spheroid ◽  
Three Dimensions ◽  
General Context ◽  
Reversed Flow ◽  
Low Incidence

This paper investigates the three-dimensional laminar boundary layer over a blunt body (a prolate spheroid) at low incidence and with reversed flow. Results reflecting the general characteristics of such a problem are presented. More significant are the features relating to the circumferential flow reversal. Some of these features confirm our early hypotheses concerning the existence of a reversed region ahead of separation and the role of the zero-cfθ line in the general context of separation in three dimensions. Other features are unexpected, including the distribution of cfμ and the shape of the separation line. Here cfθ and cfμ denote, respectively, the circumferential and meridional components of the skin friction.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals Crystal structure of 1-methyl-4-methylsulfanyl-1H-pyrazolo[3,4-d]pyrimidine

2014 ◽  
Vol 70 (12) ◽  
pp. o1281-o1281 ◽  
Author(s):  
Mohammed El Fal ◽  
Youssef Ramli ◽  
El Mokhtar Essassi ◽  
Mohamed Saadi ◽  
Lahcen El Ammari
Keyword(s):  
Crystal Structure ◽  
Title Compound ◽  
Three Dimensional ◽  
Pyrimidine Ring ◽  
Ring System ◽  
Dimensional Structure ◽  
Mirror Plane ◽  
Three Dimensional Structure ◽  
Π Interactions ◽  
Compound C

In the title compound, C7H8N4S, the non-H atoms of the pyrazolo[3,4-d]pyrimidine ring system and the methylsulfanyl group lie on a crystallographic mirror plane. In the crystal, molecules are linkedviaa number of π–π interactions [centroid–centroid distances vary from 3.452 (7) to 3.6062 (8) Å], forming a three-dimensional structure.

scholarly journals 5-Bromo-2-methyl-3-(3-methylphenylsulfinyl)-1-benzofuran

2014 ◽  
Vol 70 (3) ◽  
pp. o320-o320
Author(s):  
Hong Dae Choi ◽  
Pil Ja Seo ◽  
Uk Lee
Keyword(s):  
Dihedral Angle ◽  
Title Compound ◽  
Three Dimensional ◽  
Ring System ◽  
Π Interactions ◽  
Compound C ◽  
Dimensional Network ◽  
The Mean

In the title compound, C16H13BrO2S, the dihedral angle between the mean plane [r.m.s. deviation = 0.012 (1) Å] of the benzofuran ring system and the 3-methylphenyl ring is 84.83 (4)°. In the crystal, molecules are linkedviapairs of Br...O [3.240 (1) Å] contacts, forming inversion dimers. These dimers are linked by C—H...π interactions, forming a three-dimensional network.

scholarly journals 5-Bromo-3-ethylsulfinyl-2-(4-methylphenyl)-1-benzofuran

2014 ◽  
Vol 70 (7) ◽  
pp. o808-o808
Author(s):  
Hong Dae Choi ◽  
Pil Ja Seo ◽  
Uk Lee
Keyword(s):  
Dihedral Angle ◽  
Title Compound ◽  
Three Dimensional ◽  
Ring System ◽  
Π Interactions ◽  
Compound C ◽  
Dimensional Network ◽  
Centroid Distance

In the title compound, C17H15BrO2S, the dihedral angle between the plane of the benzofuran ring system [r.m.s. deviation = 0.004 (3) Å] and that of the 4-methylphenyl ring is 0.9 (2)°. In the crystal, molecules are linked by C—H...O, C—H...π and Br...π [3.636 (2) Å] interactions, and by π–π interactions between the 4-methylphenyl and furan rings of neighbouring molecules [centroid–centroid distance = 3.650 (2) Å], forming a three-dimensional network.

scholarly journals BenzimidazoliumL-aspartate

IUCrData ◽  
2016 ◽  
Vol 1 (5) ◽  
Author(s):  
M. Amudha ◽  
P. Praveen Kumar ◽  
G. Chakkaravarthi
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Ring System ◽  
Dimensional Structure ◽  
Carboxyl Groups ◽  
Benzimidazole Ring ◽  
Π Interactions ◽  
Graph Set ◽  
Molecular Salt

In the cation of the title molecular salt, C7H7N2+·C4H6NO4−(systematic name: 1H-benzo[d]imidazol-3-ium 2-azaniumylsuccinate), the benzimidazole ring system is almost planar (r.m.s. deviation = 0.012 Å). The cation is protonated at the N atom and the L-aspartate zwitterion is deprotonated at both carboxyl groups. In the anion, an N—H...O hydrogen bond and an N—H...O short contact generateS(6) graph-set motifs. In the crystal, the anions are linkedviathree N—H...O hydrogen bonds involving the NH3+group, forming layers parallel to theabplane. The benzimidazolium cations are linked to these layers by N—H...O hydrogen bonds. The layers are linkedviaC—H...O hydrogen bonds involving the benzimidazolium cation, forming a three-dimensional structure. There are also C—H...π interactions present involving inversion-related benzimidazolium cations.

scholarly journals 1,4-Bis(4-methoxyphenyl)naphthalene

IUCrData ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
R. Manickam ◽  
G. Jagadeesan ◽  
J. Karunakaran ◽  
G. Srinivasan
Keyword(s):  
Ring System ◽  
Molecular Packing ◽  
Dihedral Angles ◽  
Asymmetric Unit ◽  
Naphthalene Ring ◽  
Naphthalene Derivative ◽  
Π Interactions ◽  
Benzene Rings ◽  
Independent Molecules ◽  
Supramolecular Chains

The title naphthalene derivative, C24H20O2, features 4-methyoxy-substituted benzene rings in the 1 and 4 positions of the naphthalene ring system. There are two crystallographically independent molecules (A and B) in asymmetric unit. The independent molecules have very similar conformations in which the naphthalene ring systems are only slightly bent, exhibiting dihedral angles between the constituent benzene rings of 3.76 (15) and 3.39 (15)° for A and B, respectively. The pendent 4-methyoxybenzene rings are splayed out of the plane through the naphthalene ring system to which they are connected [range of dihedral angles = 59.63 (13) to 67.09 (13)°]. In the crystal, the molecular packing is consolidated by intermolecular C—H...π interactions, leading to supramolecular chains along the b axis. The chains assemble without directional interactions between them.

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