Conformational Aspects Research Articles

Synthesis and Structural Characterization of Haloaryl N‐Substituted Sugar Derivatives

AbstractWe present here the efficient preparation of 6‐N‐haloaryl‐galactosides through a reductive amination process. A complete set of 6‐deoxy‐1,2;3,4‐di‐O‐isopropylidene‐6‐N‐phenylamino‐α‐D‐galactopyranosides were obtained with a straightforward method. The products were structurally analyzed by X‐ray diffraction techniques and NMR spectroscopic data. A complete investigation of the galactosyl derivatives is described, including an unexpected N,N'‐diphenylamino by‐product. Moreover, relevant conformational aspects in solution and in the solid state are identified and discussed.

Synthesis and conformational aspects of 2-phenoxytetralones: Experimental verification and density functional theory (DFT) calculation

A series of 2-phenoxy-1-tetralones have been synthesized as conformationally constrained analogs of bioactive compounds 2-phenoxyacetophenones. A representative oxime derivative of 2-(3-methoxyphenoxy)-1-tetralone was selectively prepared and its (Z)-geometry was characterized by proton nuclear magnetic resonance (1H NMR) spectroscopy. Also, the conformational aspects of designed compounds were investigated by 1H NMR spectroscopy and density functional theory (DFT) calculations. The computational results showed that the more stable conformation in 5c is a conformer with equatorial orientation for 2-aryloxy group but the axial orientation in the related oxime 6 is predominated. Accordingly, it was demonstrated that the formation of (Z)-oxime on 1-position results in a remarkable conformational inversion on tetralin ring.

Simulation and experimental study on amphiphilic modified graphene oxide for EOR

The application of nanosheet in enhanced oil recovery (EOR) offers a practical approach to resolving some surface-related problems. In this study, theoretical calculation and experiment were combined to study the interfacial behavior and mechanism of amphiphilic modified graphene oxide. Octadecyl amine and aspartic acid were successfully grafted onto graphene oxide nanosheets by starch template method. The stability of the modified structure was verified by IR, XRD and SEM. The change of microstructure in molecular simulation can enhance the understanding of the structure of amphiphilic modified nanosheets under SEM. The contact angle experiment directly shows its amphiphilicity, which shows that the contact angle of hydrophilic surface is 34.6° and that of hydrophobic surface is 103.5°. The interfacial elasticity experiment shows that the interfacial film formed by synthetic GOTA has certain elasticity. When the concentration increases, the interfacial film formed in the adsorption process can effectively separate the oil and water phases. Based on the interfacial tension value, the ability of graphene oxide and modified graphene oxide with different concentrations to reduce the interfacial tension between distilled water and diesel oil was investigated successively. The mechanism of GOTA action was explained from the aspects of molecular structure and energy by molecular simulation. The results show that the interfacial tension fluctuates around 16 mN/m when the GOTA concentration is 0.005%, and the average interfacial tension is 17.48 mN/m when the GOTA concentration (molecular number percentage) is 0.004% in the simulation process, which is highly consistent. Further studies have shown that the interface formation energy of the system is significantly reduced after the addition of zwitterionic surfactants, and the interfacial tension can be reduced to 11.95 mN/m. With the help of molecular simulation, the adsorption mechanism of GOTA on the interface is explained from the aspects of microstructure change, interaction energy, cohesion energy, interface density and conformation. The adjustment of these interactions will directly affect the oil-water interface morphology and interfacial tension.

Parametric Analysis of Donor Activation for Glycosylation Reactions.

The chemical synthesis of complex oligosaccharides relies on efficient and highly reproducible glycosylation reactions. The outcome of a glycosylation is contingent upon several environmental factors, such as temperature, acidity, the presence of residual moisture, as well as the steric, electronic, and conformational aspects of the reactants. Each glycosylation proceeds rapidly and with a high yield within a rather narrow temperature range. For better control over glycosylations and to ensure fast and reliable reactions, a systematic analysis of 18 glycosyl donors revealed the effect of reagent concentration, water content, protecting groups, and structure of the glycosyl donors on the activation temperature. With these insights, we parametrize the first step of the glycosylation reaction to be executed reliably and efficiently.

Comprehensive computational insights on the conformations, electronic properties and binding mechanism of mescaline: A hallucinogenic molecule

In the series of computational investigations of hallucinogenic compounds particularly in unraveling their conformational aspects, mescaline is taken up in this report after having studied psilocybin and psilocin. Six conformers were identified from the relaxed scan of the dihedral angles of which two were taken up for studying their chemical properties. The two low energy conformers differed by about 0.5 kcal.mol-1 at B3LYP/cc-pVTZ and 1.5 kcal.mol-1 at CCSD/cc-PVDZ levels of theory, respectively and structurally the two conformers differ by the orientation of the alkyl amine group vis-à-vis the benzene ring via the N–H---π interaction. Natural Bond Orbital calculations unveiled the existence of intra-molecular π → π*, n → π* charge transfers, and some hyperconjugative interactions that significantly enhance the stability of mescaline. Reduced Density Gradient calculations unraveled the occurrence of strong intramolecular N–H---π interaction in the most stable conformer of mescaline. The calculated geometrical parameters and predicted structure of the most stable conformer of mescaline agree significantly well with the earlier reported conformers from X-ray studies of mescaline. The computed λmax in the UV–visible spectrum, peak positions in the proton NMR spectrum, and vibrational modes exhibit excellent agreement with the previously reported experimental findings. Moreover, we utilized molecular docking and molecular dynamics simulations to elucidate the binding mode and molecular mechanism of mescaline in comparison to other hallucinogenic molecules. Our findings revealed that mescaline displayed a favorable binding energy and induced essential conformational changes, indicating a potential common mechanism of action shared with psilocybin, another hallucinogenic compound.

DFT based Experimental investigations on the spectroscopic properties, molecular structure, and biological activity of a glucocorticoid steroid, Prednisolone

This study presents a comprehensive investigation into Prednisolone, a glucocorticosteroid drug, through vibrational analysis and DFT based quantum chemical calculations. Utilizing the DFT-B3LYP functional at the basis set 6-311++G(d,p), the research explores conformational and geometric aspects, harmonic vibrational wavenumbers, and FMO analysis. The phase angle of pseudo rotation is measured to predict the molecule's conformation. FT-IR and Raman spectra were analyzed and found that the lowering of symmetric stretching vibrations of O25-H53 and O24-H52 to 3470 and 3362 cm−1 respectively, is due to the presence of intra/intermolecular hydrogen bonding. Topology analysis (AIM, NCI,ELF, LOL) global chemical reactivity descriptor study, Hirshfeld surface analysis and electron excitation studies provide a detailed understanding of Prednisolone's molecular properties. AIM analysis proved the possibility of a strong hydrogen bond H53…….O24, because it has the minimum bond length of 1.9645 Å, accompanied by a maximum ρ value of 0.0255 a.u. The hydrogen bond O24…….H53 —– O25, indicated by blue RDG isosurfaces in NCI, with value of sign (λ2) ρ between -0.02 to -0.05 a.u, is predicted to be strong. Bandgap energy of the molecule calculated from HOMO-LUMO is 4.7105. This is well agreement with the results obtained from experimental UV-visible spectra. Molecular docking study, Drug likeness parameter analysis and ADMET properties helps in predicting the anti-inflammatory activity of the molecule.

ESG and Emotional Non-conformity of Goods in Contracts for International Sale of Goods

Purpose - It examines the potential applicability of the CISG to contracts involving the sale of goods with significant emotional value. And it addresses the issues on whether the delivery of non-compliant goods with ESG standards can be considered as an aspect of non-conformity under the CISG. Furthermore, it explores whether and how a corporate ESG codes of conduct can be duly incorporated into contract. Design/Methodology – In order to achieve the purposes of the study, it is based on a literature review which is related to the rules under the CISG as to the seller’s delivery of goods associated with emotions derived from the purchase of goods compliant with ESG standards. It mainly focuses on the rules of the CISG as to the incorporation of standard terms and the duty to deliver conforming goods. Findings – The main findings of this study are as follows. First, the view that it could be applicable based on CISG Art. 3(2) cannot be supported because emotions associated with the purchase of goods cannot be separated from the goods and treated as an independent part of the contractual obligations. Second, depending upon a matter of interpretation of contract one must sometimes incorporate minimum ESG standards into contract if the parties should have known or were expected to know in international trade for the type of transaction in question. Third, the aspects of conformity under the CISG include not only the physical conditions of the goods but also non-physical conditions which are related to various aspects of ESG standards. And as the minimum ESG standards increase due to the recent trend of social conscious consumerism, it is unreasonable not to hold the seller liable for the goods manufactured processed in a manner inconsistent with the standards only because they can be resold in a market which may damage fatally the buyer’s commercial reputation. Originality/value – It may offer guidance to both practicing lawyers and business professionals who are considering entering the sales market, particularly those dealing with goods produced or manufactured in accordance with ESG standards. In addition, it may render us an insight to newly developed or developing rules in this area and show us how they interact with each other.

Changes in aspects of hoof and distal limb conformation in foals by radiographic evaluation.

This study investigated age-related radiographic changes in the distal parts of the forelimbs by radiographic evaluation and identified the radiographic changes associated with diseases specific to foals. The hoof angle (HA), distal phalanx angle (P3A), distal phalanx palmer angle (P3PA), distal interphalangeal joint angle (DIPJA), and metacarpophalangeal joint angle (MPJA) on lateromedial radiographs of forelimbs were measured on the day after birth (Day 1); at 1, 2, 4, 6, and 8 weeks of age; and then at monthly intervals until 12 months of age. HA and P3A significantly increased from 1 day to 4 weeks and 4 weeks to 3 months of age. The P3PA increased dramatically from 1 day to 1 week, 1 week to 2 weeks, and 2 weeks to 8 weeks of age, and then decreased after 3 months of age. DIPJA significantly decreased from 1 day to 2 weeks of age before increasing from 3 to 5 months of age. MPJA increased with age until 4 weeks, slightly decreased from 2 to 4 months of age, and then gradually decreased from 4 to 6 months of age. The findings indicate that foals' forelimbs typically show flexion of the fetlock and a broken backward hoof-pastern axis just after birth, an upright fetlock until 4 months of age, and a change to a mature conformation after 6 months of age. Physiological variants were correlated with the occurrence of common foal diseases during the radiographic evaluation periods.

Large Computational Survey of Intrinsic Reactivity of Aromatic Carbon Atoms with Respect to a Model Aldehyde Oxidase.

Aldehyde oxidase (AOX) and other related molybdenum-containing enzymes are known to oxidize the C-H bonds of aromatic rings. This process contributes to the metabolism of pharmaceutical compounds and, therefore, is of vital importance to drug pharmacokinetics. The present work describes an automated computational workflow and its use for the prediction of intrinsic reactivity of small aromatic molecules toward a minimal model of the active site of AOX. The workflow is based on quantum chemical transition state searches for the underlying single-step oxidation reaction, where the automated protocol includes identification of unique aromatic C-H bonds, creation of three-dimensional reactant and product complex geometries via a templating approach, search for a transition state, and validation of reaction end points. Conformational search on the reactants, products, and the transition states is performed. The automated procedure has been validated on previously reported transition state barriers and was used to evaluate the intrinsic reactivity of nearly three hundred heterocycles commonly found in approved drug molecules. The intrinsic reactivity of more than 1000 individual aromatic carbon sites is reported. Stereochemical and conformational aspects of the oxidation reaction, which have not been discussed in previous studies, are shown to play important roles in accurate modeling of the oxidation reaction. Observations on structural trends that determine the reactivity are provided and rationalized.

Android-Based Project-Based Learning Integrated Gravimetric Analysis for Chemical Expertise Analysis of Vocational School: Development of Teaching Materials

This study aimed to produce gravimetric analysis teaching materials and determine the validity test of gravimetric analysis teaching materials. The development of teaching materials is carried out using the ADDIE development model (Analysis-Design-Development-Implementation-Evaluation). The results of the development of teaching materials are in the form of applications with the APK extension that can be run on Android smartphones. The teaching material validation test obtained the percentage of assessment which included aspects of the content of teaching materials by 84.3% (very feasible), media aspects by 83.9% (very feasible), construct aspects of teaching materials by 81.7% (very feasible), aspects the language used is 79.2% (decent), and the aspect of conformity with the PjBL is 80.9% (very decent). Of the five aspects of the gravimetric analysis validation test assessment, the teaching materials developed were very feasible, with a total percentage of 82.87%. While the readability test got a percentage of 87.3%, so it was categorized as very feasible to use

Revolutionizing water treatment, conservation, and management: Harnessing the power of AI-driven ChatGPT solutions

This study analyzes the global water crisis and the pressing need for innovation in water treatment, conservation, and management practices. It introduces potentially transformative solutions involving the use of ChatGPT to address water-related challenges. The research underscores the potential of AI-Driven ChatGPT applications in enhancing water management schemes through real-time insights, optimization of resource usage, and predictive maintenance. The paper dilates upon the role of ChatGPT in improving water quality control, enriching decision-making systems, optimizing water usage, and promoting precision irrigation. It also discusses various scenarios where ChatGPT has been applied in this regard, such as in Klir Comply and its integration into Rammas. The study further discusses the significant water consumption and environmental implications of AI models like ChatGPT and suggests tangible solutions such as employing renewable energy sources and water recycling systems. Additionally, it delves into ethical and regulatory implications of integrating AI-Driven ChatGPT solutions in water management, covering aspects of data privacy, transparency, accountability, and conformity to international standards. It emphasizes the need for concerted efforts to construct a responsible AI governance model and highlights the importance of education and awareness regarding AI ethics and regulations.

Analysis of Errors in Using Words and Punctuation on Housing Advertising Banners in Jatiasih District, Bekasi City and Their Implications for Indonesian Language Learning

This study aims to analyze the errors in the use of words and punctuation on housing advertisement banners. The purpose of this study is to find out and describe the forms of word errors and punctuation on housing advertisement banners. This type of research is qualitative research which describes the data using a series of sentences. The method in this study is a qualitative method based on the philosophy of postpositivism, used to research on natural object conditions, (as opposed to experiments) where the researcher is the key instrument. Data collection techniques are carried out triangulation (combined), data analysis is inductive/qualitative, and the results of qualitative research emphasize eating more than generalization. The research technique used is to describe and understand the existence of errors in the use of words and punctuation on housing advertisement banners. Based on the results of the study, it was found that the form of errors in the use of the word aspects of accuracy, and aspects of conformity was found. Errors in the use of punctuation consisting of: (1) errors in the use of punctuation marks (.), (2) errors in the use of punctuation marks (,), (3) errors in the use of punctuation marks (-), (4) errors in the use of punctuation marks punctuation (-), (5) errors in the use of exclamation marks (!), (6) errors in the use of quotation marks (“…”), (7) errors in the use of single quotation marks ('...') , and (8) errors in using slash punctuation (/). In writing one must understand the rules of writing, one of which is the use of standard words and the use of PUEBI, so that writing complies with good and correct rules in the use of capital letters, punctuation marks , and word writing

Improving machine learning force fields for molecular dynamics simulations with fine-grained force metrics.

Machine learning force fields (MLFFs) have gained popularity in recent years as they provide a cost-effective alternative to abinitio molecular dynamics (MD) simulations. Despite a small error on the test set, MLFFs inherently suffer from generalization and robustness issues during MD simulations. To alleviate these issues, we propose global force metrics and fine-grained metrics from element and conformation aspects to systematically measure MLFFs for every atom and every conformation of molecules. We selected three state-of-the-art MLFFs (ET, NequIP, and ViSNet) and comprehensively evaluated on aspirin, Ac-Ala3-NHMe, and Chignolin MD datasets with the number of atoms ranging from 21 to 166. Driven by the trained MLFFs on these molecules, we performed MD simulations from different initial conformations, analyzed the relationship between the force metrics and the stability of simulation trajectories, and investigated the reason for collapsed simulations. Finally, the performance of MLFFs and the stability of MD simulations can be further improved guided by the proposed force metrics for model training, specifically training MLFF models with these force metrics as loss functions, fine-tuning by reweighting samples in the original dataset, and continued training by recruiting additional unexplored data.

Towards understanding the interaction of quercetin with chitosan-phytate complex: An experimental and computational investigation

Spectroscopic and structural properties of quercetin (QE) encapsulated in chitosan-phytate anion (CT-PA) nanoparticles were investigated, and an all-atom model was employed for molecular dynamics simulations to broaden the perspective on the conformational and energetics aspects regarding the quercetin-chitosan complexation. Quercetin binding to the free chitosan chains and its encapsulation in the nanoparticle obtained in the presence of the phytate anion was confirmed using dynamic light scattering and Fourier-transform infrared spectroscopy, and a considerably hindered rotational motion of the probe bound to the chitosan strand was demonstrated by the steady-state and anisotropy fluorescence measurements. While morphologies ranging from nearly spherical nanoparticles to nanofibrils were observed through atomic force microscopy upon increasing the chitosan content, a high encapsulation efficiency of QE, weakly dependent on the size and shape of CT-PA nanoparticles, was found. Simulation-based structural and energetics predictions indicated a similar H bond pattern for the QE binding to the chitosan strands, either in a free state or reticulated with the aid of the phytic anion. Additional crosslinker-assisted retention of quercetin in the chitosan network, as well as an enhanced electrostatic contribution to the binding free energy obtained at encapsulation, were derived from molecular dynamics simulations.

Conformational and Supramolecular Aspects in Chirality of Flexible Camphor-Containing Schiff Base as an Inducer of Helical Liquid Crystals.

The experimental and theoretical study of influence of the conformational state and association on the chirality of the stereochemically nonrigid biologically active bis-camphorolidenpropylenediamine (CPDA) and its ability to induce the helical mesophase of alkoxycyanobiphenyls liquid-crystalline binary mixture was carried out. On the basis of quantum-chemical simulation of the CPDA structure, four relatively stable conformers were detected. A comparison of the calculated and experimental electronic circular dichroism (ECD) and 1H, 13C, 15N NMR spectra, as well as specific optical rotation and dipole moments, allowed to establish the most probable trans-gauche conformational state (tg) of dicamphorodiimine and CPDA dimer with a predominantly mutually parallel arrangement of molecular dipoles. The induction of helical phases in LC mixtures based on cyanobiphenyls and bis-camphorolidenpropylenediamine was studied by polarization microscopy. The clearance temperatures and the helix pitch of the mesophases were measured. The helical twisting power (HTP) was calculated. The decrease in HTP with increasing dopant concentration was shown to be connected with the CPDA association process in the LC phase. The effect of camphor-containing chiral dopants of various structures on nematic LCs was compared. The values of the permittivity and birefringence components of the CPDA solutions in CB-2 were measured experimentally. A strong effect of this dopant on the anisotropic physical properties of the induced chiral nematic was established. A significant decrease in the dielectric anisotropy was associated with the 3D compensation of the LC dipoles during the formation of the helix.

Pengembangan LKPD Berbasis Kemampuan Berpikir Kritis pada Materi Pecahan di Kelas V SDN 34 Pontianak Selatan

The study aims to produce worksheet based on students critical thinking skills on addition and subtraction of fractions whit different denominators in class V SDN 34 South Pontianak. Research and development (RnD) methods by adapting the Thiagarajan development model (define, design, development and dissemination). The data sources for this research were the results of the validation of 3 validators, the results of the practicality questionnaire, and the result of the student worksheet trials. The data collection technique for this research was a validator validation questionnaire, practicality questionnaire, and test questions for students. The result of the study show that during the process of developing LKPD based on critical thinking skills, there are four stages, namely define, design, development and dissemination. The validity of the average percentage of LKPD from the learning aspect (material) is 83% whit very valid criteria, from the appearance (design) aspect it is 74% with valid criteria, and the aspect of conformity with critical thinking skills is 90% whit very valid criteria. The practicality of using LKPD based on small-scale critical thinking skills is 3,9 in the practical category, and the practicality of using LKPD based on large scale critical thinking skills is 3,9 in the practical category. The mastery level of small scale trials obtained an average percentage of 100% completeness whit very high criteria and large-scale trials obtained an average percentage of 85,7% completeness with very high criteria.

Factor analysis of evaluated and linearly scored traits in Swedish Warmblood horses.

Assessment protocols to describe the various aspects of conformation, gait and jumping traits on a linear scale were introduced at young horse tests for Swedish Warmblood horses in 2013. The traits scored on a linear scale are assumed to be less subjective and more easily compared across populations than the traditional evaluated traits that are scored relative to the breeding goal. However, the resulting number of traits is considerable, and several of the traits are correlated. The aim of this study was to investigate the interrelationship between the different evaluated and linearly scored traits in Swedish Warmbloods using factor analysis. In total, 20,935 horses born 1996-2017 had information on evaluated traits, and 5450 of these also had linearly scored trait records assessed since 2014 when the protocol was updated. A factor analysis with varimax rotation was performed separately for evaluated and linearly scored traits using the Psych package in R. Height at withers was included in both analyses. A total of four factors for evaluated traits and 14 factors for linearly scored traits were kept for further analysis. Missing values for individual traits in horses with linearly scored trait records were imputed based on correlated traits before factor scores were calculated using factor loadings. Genetic parameters for, and correlations between, the resulting underlying factors were estimated using multiple-trait animal models in the BLUPF90 package. Heritability estimates were on a similar level as for the traits currently used in the genetic evaluation, ranging from 0.05 for the factor for linearly scored traits named L.behaviour (dominated by traits related to behaviour) to 0.59 for the factor for evaluated traits named E.size (dominated by height at withers and conformation). For both types of traits, separate factors were formed for jumping and gait traits, as well as for body size. High genetic correlations were estimated between such corresponding factors for evaluated traits and factors for linearly scored traits. In conclusion, factor analysis could be used to reduce the number of traits to be included in multiple-trait genetic evaluation or in genomic analysis for warmblood horses. It can also contribute to a better understanding of the interrelationships among the assessed traits and be useful to decide on subgroups of traits to be used in several multiple-trait evaluations on groups of original traits.

Conformational aspects in the formation of structures of the backbone of polypeptide chains in proteins. Relationship between conformational stability/lability and β-turns

To assess the nature of the relationship between the integral conformational stability of tetrapeptides and the main types of β-turns (which are also tetrapeptides), calculations were performed using spectrum diagrams and asymmetry in the distribution of conformationally stable and unstable tetrapeptides. It was shown that type I', II, and II' β-turns are comprised of predominantly conformationally labile peptides, that is consistent with the predetermined nature of their structure as described earlier. As previously shown in our study, in this case the conformation is imposed by external conditions (namely the cycle closuring) and the prevalence of conformationally labile peptides facilitates the formation of the structure by virtue of external factors. Type I β-turn is an exception: peptides with different conformational lability are fairly evenly distributed. Most likely, this indicates that the formation of the type I β-turn is not predetermined.

Conformational Aspects in the Formation of Structures of the Backbone of Polypeptide Chains in Proteins: the Relationship between Conformational Stability/Lability and β-Turns

Conformational Aspects in the Formation of Structures of the Backbone of Polypeptide Chains in Proteins: the Relationship between Conformational Stability/Lability and β-Turns

Pengembangan LKPD HOTS Bernuansa Sikap Tanggung Jawab Materi Pecahan Kelas V SDN 12 Pontianak Kota

This study aims to produce a HOTS Student Worksheet design with a nuanced attitude of responsibility in the material for adding and subtracting fractions for class V SDN 12 Pontianak Kota. The research method used is research and development (RnD) by adapting the Thiagarajan 4D development model (define, design, development and dissemination). The data source for this research is the results of the validation of the three validators and the results of the student worksheet trials. The data collection technique for this research was a validator validation questionnaire, test questions for students, as well as documentation on the LKPD used by the teacher. The results of the research show that during the process of developing HOTS LKPD with a nuanced attitude of responsibility it is carried out only in three stages, namely the define, design and development stages. The percentage of LKPD validity criteria from the material aspect has an average of 4 with very valid criteria, from the language aspect it is 4 with very valid criteria, from the display aspect it is 3.86 with very valid criteria, and from the aspect of conformity with the responsibility indicator it is 4 with very valid criteria. The percentage of the criteria for the completeness level of students' scores in the first trial obtained a completeness percentage of 100% with very high criteria and the second trial obtained a completeness percentage of 73% with high criteria.