Helix Type Research Articles

Solvent-controlled assembly of helical coordination polymers based on lactate synthon from two-dimensional layer to three-dimensional framework

Compound (R)-4-(1-carboxyethoxy)-2-methylbenzoic acid ((R)-H2cma) was prepared from (S)-methyl lactate and 4-hydroxy-2-methylbenzoic acid. (R)-H2cma as chiral synthon assembled with 1,3-di(pyridin-4-yl)propane (1,3-dpp) and Ni2+ ions to obtain helical chiral complexes {[Ni2((R)-cma)2(1.3-dpp)2]·H2O}n (HU18-R) and {[Ni2((R)-cma)2(1.3-dpp)2(H2O)]·3H2O}n (HU19-R) in different solvent systems. Single crystal tests revealed that HU18-R is a two-dimensional (2D) structure with two independent Ni2+ centers and HU19-R is a three-dimensional (3D) framework containing dinuclear [Ni2(CO2)2(H2O)]2+ clusters. Four types of helices were formed in HU18-R and HU19-R by chiral transfer or induction. In HU18-R, small right-handed (R)-cma-Ni chain and large right-handed (R)-cma-Ni-1.3-dpp chain were constructed by chiral transfer. For HU19-R, helical nano-channel based on achiral 1.3-dpp ligands and Ni2+ ions was obtained from chiral induction method and small (R)-cma-Ni chain was built from chiral transfer. As semi-conducting materials, HU18-R and HU19-R indicate strong absorption capacity for UV–vis light and low-impedance properties. Under UV light, they have noticeable catalytic effects for degradation of methylene blue (MB). Moreover, magnetic tests confirmed that HU18-R and HU19-R have ferromagnetic and antiferromagnetic properties, respectively.

Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure.

A fundamental goal in evolutionary biology and population genetics is to understand how selection shapes the fate of new mutations. Here, we test the null hypothesis that insertion-deletion (indel) events in protein-coding regions occur randomly with respect to secondary structures. We identified indels across 11,444 sequence alignments in mouse, rat, human, chimp, and dog genomes and then quantified their overlap with four different types of secondary structure-alpha helices, beta strands, protein bends, and protein turns-predicted by deep-learning methods of AlphaFold2. Indels overlapped secondary structures 54% as much as expected and were especially underrepresented over beta strands, which tend to form internal, stable regions of proteins. In contrast, indels were enriched by 155% over regions without any predicted secondary structures. These skews were stronger in the rodent lineages compared to the primate lineages, consistent with population genetic theory predicting that natural selection will be more efficient in species with larger effective population sizes. Nonsynonymous substitutions were also less common in regions of protein secondary structure, although not as strongly reduced as in indels. In a complementary analysis of thousands of human genomes, we showed that indels overlapping secondary structure segregated at significantly lower frequency than indels outside of secondary structure. Taken together, our study shows that indels are selected against if they overlap secondary structure, presumably because they disrupt the tertiary structure and function of a protein.

Dry reforming process using microwave plasma generator with high carbon dioxide conversion efficiency for syngas production

The proposed CO2 reforming solution has improved CO2 conversion efficiency by developing a new double helix type plasma generator (DHTPG) to preheat the discharge gas and increase residence time of CO2 at DHTPG. In addition, injecting CH4 independently allows for a stable increase in the temperature of the CO2 plasma in the microwave plasma generator compared with other conventional methods. To verify the performance of the DHTPG, we experimentally investigated the distribution of the plasma gas temperature using an enthalpy probe system as a function of the specific energy input, which is a key parameter for understanding the mechanisms of CO2 reforming of CH4. We performed the CO2 reforming of CH4 using the newly designed plasma generator and a comparative analysis of its characteristics with those of other plasma generators. Without catalyst materials, our method significantly enhanced the CO2 conversion efficiency to 91.4 % with an energy efficiency of 67 % at a specific energy input of 245 kJ/mol. The main advantage of our method is an increase in energy-consumption selectivity, in which the energy injected through the plasma decomposes CO2 rather than CH4. In addition, it reduces the energy required to stably maintain the plasma to improve energy efficiency.

Distinguishing Different Hydrogen-Bonded Helices in Proteins by Efficient 1H-Detected Three-Dimensional Solid-State NMR.

Helical structures in proteins include not only α-helices but also 310 and π helices. These secondary structures differ in the registry of the C═O···H-N hydrogen bonds, which are i to i + 4 for α-helices, i to i + 3 for 310 helices, and i to i + 5 for π-helices. The standard NMR observable of protein secondary structures are chemical shifts, which are, however, insensitive to the precise type of helices. Here, we introduce a three-dimensional (3D) 1H-detected experiment that measures and assigns CO-HN cross-peaks to distinguish the different types of hydrogen-bonded helices. This hCOhNH experiment combines efficient cross-polarization from CO to HN with 13C, 15N, and 1H chemical shift correlation to detect the relative proximities of the COi-Hi+jN spin pairs. We demonstrate this experiment on the membrane-bound transmembrane domain of the SARS-CoV-2 envelope (E) protein (ETM). We show that the C-terminal five residues of ETM form a 310-helix, whereas the rest of the transmembrane domain have COi-Hi+4N hydrogen bonds that are characteristic of α-helices. This result confirms the recent high-resolution solid-state NMR structure of the open state of ETM, which was solved in the absence of explicit hydrogen-bonding restraints. This C-terminal 310 helix may facilitate proton and calcium conduction across the hydrophobic gate of the channel. This hCOhNH experiment is generally applicable and can be used to distinguish not only different types of helices but also different types of β-strands and other hydrogen-bonded conformations in proteins.

Describing the Pollen Content in the Gastrointestinal Tract of Vespa velutina Larvae.

Vespa velutina is an invasive species that exhibits flexible social behavior, which may have contributed to its introduction in several European countries. It is important to understand its behavior in order to combat the effects of its introduction in different areas. This implies knowing the resources that it uses during its biological cycle. Hornets require protein resources taken from insects and organic matter as well as carbohydrates as an energy source to fly and also to forage for food and nest-building materials. The gastrointestinal tract of adults and larvae contains a wide variety of pollen types. The identification of this pollen in larvae collected from nests could offer information about the plant species that V. velutina visits as a foraging place. The main objective of this research was to study the pollen content in the gastrointestinal tract of larvae. Patterns of pollen content and pollen diversity were established according to the nest type, altitude, season, and location in the nest comb. The abundance of pollen types such as Eucalyptus, Castanea, Foeniculum vulgare, Hedera helix, Taraxacum officinale, Echium, or Cytisus pollen type stands out in many of the samples.

Balancing and Alignment Analysis of Vertical Wind Turbine Helix Type and Savonius Type

Electrical energy is one of the basic needs that is very important in life, in addition to the physiological development of living things, electricity is also an input for various efforts or activities in order to produce something for survival. Therefore, renewable energy that is more environmentally friendly and an inexhaustible source of energy is needed, namely wind energy. This power generator is called a wind turbine with a vertical shaft. This turbine converts wind energy into mechanical and electrical. In order to obtain a turbine design with high efficiency. It is also necessary to balance and align each component frame attached to the turbine rotor to produce a perfect/ideal rotation, so as to minimize the occurrence of vibrations caused by the imbalance. the results of calculations with the analytical method on Darrius Helix type obtained value = 0.125 Newton, and = 0.175 Newton, and the value of the angle = 63.43490. Alignment testing is carried out to determine the value of the misalignment between one blade with another blade. The results of the balancing test with the blade ballast obtained additional value, the blade D was 70 grams and the results from the plate addition test were obtained according to the calculation of the analytical method but also less than the maximum requiring additional load on the blade body to get blade A = 12 grams, blade B = 0, blade C = 40 grams, and a spoon D = 90 grams. For the results and discussion of the balancing and alignment method on the savonius type using the static balancing and alignment method using a dial indicator, the values obtained are in the fields A and B, the addition of mass is 59,007 grams and 59.007 grams with angles A and B 11.88 ° , and the value The misalignment deviation in the A, B and center planes is A: 4mm, B: 0.04mm, middle: 0.52mm, while the shaft alignment value is 0 because the value of the alignment of the shafts is the same or parallel.

Four-connected chiral coordination polymers embedding helices constructed from enantiomeric lactate synthons: fluorescent and photo-catalytic properties

Lactic acid units were attached to 3-bromo-4-hydroxybenzoate to obtain a pair of enantiomers (R)-3-bromo-4-(1-carboxyethoxy)benzoic acid ((R)-H2bba) and (S)-3- bromo-4-(1-carboxyethoxy) benzoic acid ((S)-H2bba). (R)-H2bba and (S)-H2bba as chiral ligands constructed CCPs {[Zn((R)-bba)(4,4′-bpy)]·H2O}n (HU10-R), {[Zn((S)-bba)(4,4′-bpy)]·H2O}n (HU10-S), [Co((R)-bba)(1,3-dpp)]n (HU11-R) and [Co((S)-bba)(1,3-dpp)]n (HU11-S) (4,4′-bpy = 4,4′-bipyridine, 1,3-dpp = 1,3-di(pyridine−4-yl)propane), respectively. Single crystal diffraction test revealed that all these complexes all 3D helical frameworks with dia net. Zn(Ⅱ) centers, (R)-bba2- anions and/or 4,4′-bpy ligands are bridged together to build three types of helixes around 41 screw axis in HU10-R, while Zn(Ⅱ) centers, (S)-bba2- anions and/or 4,4′-bpy ligands form enantiomeric helixes around 43 screw axis in HU10-S. Furthermore, (R)-bba2- and (S)-bba2- anions are respectively connected by Co(Ⅱ) centers to obtain a pair of small helical chains in complexes HU11-R and HU11-S, while 1,3-DPP ligands and Co(Ⅱ) centers construct another pair of large helical chains around 41screw axis. Further studies conclusively found that HU10-R indicates red shift fluorescent phenomenon and nonlinear optical (NLO)-active property. Moreover, HU11-R has low resistance in charge transportation and catalytic activity in degradation of dyes under ultraviolet light.

Non-lightlike Helices Associated with Helical Curves, Relatively Normal-Slant Helices and Isophote Curves in Minkowski 3-space

In this paper, we introduce a new type of non-lightlike general helix that we name non-lightlike associated helix which is associated with a non-lightlike special surface curve. By using the Darboux frame of a surface curve, we generate the position vector of a non-lightlike associated helix in parametric form. We investigate special cases when the non-lightlike surface curve is a helical curve, a relatively normal-slant helix or an isophote curve. In every case, we obtain the position vector of the non-lightlike associated helix by solving differential equations and examples are given for the achieved results.

Making Sense of Helices: Right and Wrong Models in Science and Art

Helices are ubiquitous in art and nature. Independent of their pitch and sense of rotation (handedness), helices in sculpture, painting, architecture, scientific illustrations, conference announcements, logos, and advertising are eye-catching and aesthetically pleasing. Helices can turn either clockwise (right-handed helix) or anti-clockwise (left-handed helix). The [Formula: see text]-helix formed by l-amino acids and the double helices formed by [Formula: see text]-d-2′-deoxyribonucleic acid (A- and B-form DNA) and [Formula: see text]-d-ribonucleic acid (A-form RNA) are all right-handed. Artistic license provides the freedom to create helices of any shape and sense; indeed, many helical sculptures do not follow the natural convention observed in proteins and DNA. What is more surprising, given that models of the [Formula: see text]-helix and the DNA double helix were published over 70 years ago, is how common left-handed DNA double helices are in the context of scientific papers and books as well as in popular science writing and reporting. In all cases except for left-handed Z-DNA, the use of left-handed helices in scientific illustrations or models is incorrect. Here, we revisit the helix types adopted by peptides, DNA, and RNA, and review examples of right and wrong helical models in science, art, and elsewhere.

Quantum spin helices more stable than the ground state: Onset of helical protection

Topological magnetic structures are promising candidates for resilient information storage. An elementary example is spin helices in one-dimensional easy-plane quantum magnets. To quantify their stability, we numerically implement the stochastic Schr\"odinger equation and time-dependent perturbation theory for spin chains with fluctuating local magnetic fields. We find two classes of quantum spin helices that can reach and even exceed ground-state stability: spin-current-maximizing helices and, for fine-tuned boundary conditions, the recently discovered ``phantom helices.'' Beyond that, we show that the helicity itself (left or right rotating) is even more stable. We explain these findings by separated helical sectors and connect them to topological sectors in continuous spin systems. The resulting helical protection mechanism is a promising phenomenon for stabilizing helical quantum structures, e.g., in ultracold atoms and solid-state systems. We also identify a third type of phantom helix in the system.

Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic.

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic.

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

Damping vibration in three-dimensional helically tapered rod with power-law thickness

Tapered structure with power-law thickness has been regarded as an efficient approach for passive vibration control. In this paper, a three-dimensional (3D) helically tapered structure with power-law feature is proposed to reduce the vibration in rod structure. Compared with the traditional one-dimensional tapered rod, this novel helix type can compress the length of tapered region by the coiling configuration and transform the flexural wave modes into various complex modes. Drawing on its folded characteristic, the helix structure can generate highly efficient space utilization and achieve a superior vibration attenuation effect in the low frequency band. Numerical investigations on the dynamics and reflection coefficient analyses of different rod types are conducted and the reduction mechanism of 3D helically tapered rod is revealed. It is found that the larger helical radius can contribute to the reduction in low-frequency vibration, but it deteriorates the vibration performance in broadband. To overcome this “sudden collapse” phenomenon in the damping performance caused by the low stiffness, the novel step helically tapered rod is presented. According to the introduced multimodal and multidirectional mode-coupling effects, this step 3D helix structure not only makes up for the shortcoming of vibration control in low frequency range, but also further improves the innate advantage of reduction effect in the high frequency band. Meanwhile, parametric studies of step 3D helically tapered rod are performed and the effect of different constituent materials is discussed to expand the utility. To validate these analyses, experimental tests are also conducted. The results demonstrate its remarkable vibration reduction in broadband frequency.

Chalcogen-Bond-Induced Double Helix Based on Self-Assembly of a Small Planar Building Block.

As a rule, helical structures at the molecular level are formed by non-planar units. This makes the design of helices, starting from planar building blocks via self-assembly, even more fascinating. Until now, however, this has only been achieved in rare cases, where hydrogen and halogen bonds were involved. Here, we show that the carbonyl-tellurium interaction motif is suitable to assemble even small planar units into helical structures in solid phase. We found two different types of helices: both single and double helices, depending on the substitution pattern. In the double helix, the strands are connected by additional Te⋅⋅⋅Te chalcogen bonds. In the case of the single helix, a spontaneous enantiomeric resolution occurs in the crystal. This underlines the potential of the carbonyl-tellurium chalcogen bond to generate complex three-dimensional patterns.

Alanine: from the usual to the unexpected

Data from the experiments provides a possibility to talk about anomalously large contribution of alanine to the stability of an alpha-helix and other protein conformations. Independent data (and also experimental ones) suggest that alanine plays an especially big role in stabilization of the alpha-helix. This can be seen through the positive contribution of alanine both to the entropy of the system and to the enthalpy. The high contribution of alanine to the enthalpy of formation of the alpha helix contradicts the generally accepted view that the entropy should decrease during the formation of regular structures in proteins. Among three types of helices in proteins, alanine stabilizes two secondary structures: the alpha helix and the left helix of polyproline II, and in the case of fibrillar proteins, alanine also stabilizes the beta sheet. The stabilizing effect of alanine on the alpha helix structure extends to both natively unfolded proteins and alpha helix-support conjugates. Thus, it is no exaggeration to say that formation of secondary structure relies on alanine. The revealed contradictions are of paradoxical nature and yet there is no interpretation of the above-mentioned findings (first of all, substantiation of the contribution of alanine to the enthalpy of fusion in terms of fundamental physics) so far to resolve them. Meanwhile, the data and comments presented in this work hold out the promise of progress in resolving the revealed contradictions.

Azepine-Embedded Seco-Hexabenzocoronene-Based Helix Nanographenes: Access to Modification of the Core by N–H Functionalization

Contorted polycyclic aromatic hydrocarbons (PAHs) or nanographenes (NGs) have received increasing attention and are mostly prepared by "bottom-up" strategies. Apparently, systematically tuning the properties of NGs for application is important but challenging. Here, a new type of helix, azepine-embedded NGs, were designed and synthesized by the introduction of NH into the hexa-peri-hexabenzocoronene (HBC) core. We demonstrate that this nitrogen-doped NG can be functionalized via N-H derivatization. Through modifications to the NH site with a chiral auxiliary reagent, optical resolution of the chiral NG was achieved. Meanwhile, it was found that by introducing various aryl groups with electron-donating or electron-withdrawing substituents, the emission intensity and the fluorescence mechanism can be modulated. Compared to the original NH-containing NG, the modified derivative exhibited improved fluorescence efficiency and tunable emission wavelength. A functionalized structure of benzoic acid with considerably improved fluorescence efficiency, hydrophilicity, and membrane permeability to stain the live cells was proved.

MATLAB-Based Visualization of Helical Structures and Their Applications

A helix is a type of smooth space curve, i.e. a curve in three-dimensional space. This study aims to present a MATLAB-based approach to visualize helical structures and to demonstrate their applications in various fields. As a qualitative study, primary and secondary sources of data have been consulted. Primarily, observing the real-life activities of humans and secondly, the analysis of archival documents such as related research articles, analytical books, and related reports. In conclusion, most of the architectural work in the world is possible by different types of geometrical design through the helix. It also found that we can visualize the different types of helices by using MATLAB in mathematics teaching. The implication of helix is everywhere in different fields and areas such as constructing a basket, screw, etc. Finally, we used helical concepts related to daily life activities in the field of instruction in the mathematics classroom.

Desain Dan Simulasi Turbin Angin Savonius Dengan Konfigurasi Rotor Tipe L Dan Tipe Helix Sebagai Sumber Listrik Lampu PJU Pelabuhan Perikanan Cikidang Pangandaran Jawa Barat

Cikidang Fishing Port, Pangandaran, West Java is located in the southern region of Java island which is directly opposite the Indian Ocean which has the potential for energy development, one of which is from wind. Wind is one of the natural resources that can be used as an alternative power generation source as a substitute for conventional fuel. From the results of observations on the average wind speed for seven days of v = 4.8 m/s. Based on the results of observations, a vertical axis wind turbine, namely Savonius, is planned as the drive of the power plant generator, with configurations in the shape of the rotor, namely the L type and helix type. In type L with a diameter of 1.1 meters, a height of 1.4 meters can receive kinetic energy = 60.96 Joules which has the potential to produce a rotor power of 110.87 Watts. While in the Helix type with a diameter of 1.1 meters, a height of 1.4 meters can receive 82,63 Joules which has the potential to produce a rotor power of 159.32 Watts. In the static structural simulation, for the Savonius L type wind turbine rotor with Aluminum Alloy material, it showed a total deformation of 12.239 mm, an equivalent elastic strain of 2.1252 x 10-4 mm, and an equivalent stress of 14.973 MPa at a rotor rotation speed of 83.4 RPM with a wind thrust force of 25.4 Newton. The Savonius Helix type wind turbine rotor with Aluminum Alloy material showed a total deformation of 11.74 mm equivalent elastic strain of 1.5941 x 10-5 mm, and an equivalent stress of 18.75 MPa at a rotor rotation speed of 83.4 RPM with a wind thrust force of 34.43 Newton.

Folding Coarse-Grained Oligomer Models with PyRosetta.

Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta's ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.

In situ observation of the magnetization configuration and reversal in cylindrical nanowires

Curvilinear magnetic structures often have unique magnetic behavior compared to their rectilinear counterparts. This is due to the unique curvilinear boundary conditions as well as the curvature induced Dzyaloshinskii–Moriya-like interaction and the curvature induced anisotropy. The effects of a curvilinear geometry are best studied in 3D structures, where the curvature can have a significant spatial extent. Of these 3D structures, the simplest structure to study is the cylindrical nanowire. Here, we have simulated the magnetization reversal in cylindrical NiFe nanowires and present in situ Lorentz TEM images to support the findings of the simulations. We studied the domain formation and reversal of nanowires with two distinct diameters that give rise to a different reversal behavior. We have, thus, found that the zero-field magnetization configuration in these wires can take on a double helix type of configuration. The reversal in these structures then proceeds through the winding and unwinding of these helical configurations rather than through domain wall propagation.