Studies In Physical Chemistry Research Articles

A white cell based broadband transient UV-vis absorption spectroscopy with pulsed laser photolysis reactors for chemical kinetics under variable temperatures and pressures

UV-vis spectroscopy is widely used for kinetic studies in physical chemistry, as species’ absolute cross-sections are usually less sensitive to experimental conditions (i.e., temperature and pressure). Here, we present the design and characterization of a multipass UV-vis absorption spectroscopy white cell coupled to a pulsed-laser photolysis flow reactor. The glass reactor was designed to facilitate studies of gas phase chemical reactions over a range of conditions (239–293 K and 10–550 Torr). Purged windows mitigate contamination from chemical precursors and photolysis products. We report the measured impact of this purging on temperature uniformity and the absorption length and present some supporting flow calculations. The combined optical setup is unique and enables the photolysis laser to be coaligned with a well-defined absorption pathlength probe beam. This alignment leverages the use of one long-pass filter to increase the spectrum flatness and increase the light intensity vs other systems that use two dichroic mirrors. The probe beam is analyzed with a dual exit spectrograph, customized to split the light between an intensified CCD and photomultiplier tube, enabling simultaneous spectrum and single wavelength detection. This multipass system yields a pathlength of ∼450 cm and minimum observable concentrations of ∼3.7 × 1011 molecule cm−3 (assuming cross-sections ∼1.2 × 10−17 cm2). The temperature profile across the reaction region is ±2 K, defined by the worst-case temperature of 239 K, validated by measurements of the N2O4 equilibrium constant. Finally, the system is implemented to study the simplest Criegee intermediate, demonstrating the instrument performance and advantages of simultaneous spectrum and temporal profile measurements.

C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids.

Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.

Physical Chemistry Study of Graphite Liquid Exfoliation through (π–π) Interaction by (n)-Annulene

Physical Chemistry Study of Graphite Liquid Exfoliation through (π–π) Interaction by (n)-Annulene

Characterizing centrosymmetric two-ring PAHs using jet-cooled high resolution mid-infrared laser spectroscopy and anharmonic quantum chemical calculations.

The presence of Polycyclic Aromatic Hydrocarbon (PAH) molecules in the interstellar medium, recently confirmed by the detection of cyano-naphthalenes, has renewed the interest of extensive spectroscopic and physical-chemistry studies on such large species. The present study reports the jet-cooled rovibrational infrared study of three centrosymmetric two-ring PAH molecules, viz., naphthalene (C10H8), [1,5] naphthyridine (C8H6N2), and biphenyl (C12H10), in the in-plane ring C-H bending (975-1035cm-1) and C-C ring stretching (1580-1620cm-1) regions. For the two most rigid PAHs, the accuracy of spectroscopic parameters derived in ground and several excited states (six for naphthalene and six for [1,5] naphthyridine) has significantly improved the literature values. In addition, comparison between experiments and quantum chemical calculations confirms the predictive power of the corrected calculated rotational parameters. The more flexible structure of biphenyl makes the analysis of high resolution jet-cooled spectra of ν19 and ν23 modes recorded at about 1601 and 1013cm-1, respectively, particularly challenging. The presence of three torsional vibrations below 120cm-1 together with small values of the rotational constants prevented us from determining the ground and v19 = 1 excited rotational constants independently. In the ν23 band region, the presence of two bands rotationally resolved and separated by only 0.8cm-1 raises the question of possible splittings due to a large amplitude motion, most probably the torsion of the aliphatic bond between the two phenyl rings.

Profesor Stanisław Komornicki (1949-2016)

PROFESSOR STANISŁAW KOMORNICKI (1949-2016): A MEMOIR
 The aim of this article is to present the figure of Prof. Dr. hab. Stanisław Komornicki (1949-2016), who worked at the University of Science and Technology in Kraków and the University of Applied Sciences in Tarnów. The professor was born, raised, and educated in Krakow (in the years 1967-1968 and 1971-1972, he graduated from full-time master’s studies in physical chemistry at the Faculty of Mathematics, Physics and Chemistry of the Jagiellonian University). He started his scientific work and career in Kraków (first at the Environmental Laboratory of Physicochemical and Structural Research of the Jagiellonian University, then at the University of Science and Technology in Kraków). He attended many symposia and conferences as part of his studies, but also participated in competitive sports, and later served as a judge of rowing. He was associated with the city of Tarnów as an academic teacher, vice-rector, and then rector at the University of Applied Sciences in Tarnów, which was established in the late-1990s. S. Komornicki also participated in the works of the oldest sports federation in the world, Fédération Internationale des Sociétés d’Aviron – FISA (International Federation of Rowing Societies), as a member of the Arbitration Commission. He was on the jury of the World Rowing Championships in 1989, 1994, 1995, 1999, the 2000 World Rowing World Championships, the Olympic Games in Athens (2004), Beijing (2008) and in London (2012).

A Physical Chemistry Study of Black Powder Materials by Solution Combustion Synthesis Method

A study on the synthesis of black powder (La2NiO4) material using the solution combustion synthesis method at a variation of synthesis temperature of 60, 70, and 80°C was carried out. It produces a mass of black powder of 2 grams by four times of synthesis process. Then, material characterization was performed on the black powder samples obtained by using X-ray Diffraction (XRD) to determine the phases formed, Scanning Electron Microscopy - Energy Dispersive X-ray Spectroscopy (SEM-EDS) to determine the morphology and analyze the composition elemental on the microscale and Fourier Transform Infra-Red (FTIR) to determine chemical bonds. From the whole black powder sample, XRD analysis showed the phases of Dilantanum Nickel Tetraoxide (La2NiO4), Nickel Oxide (NiO), Lanthanum Oxide (La2O3), and Lanthanum Oxide Ht x-form (La2O3 Ht (x-form)). In addition, it was seen from the visible compositions of the phases that the NiO phase looks more dominant and the variation of the synthesis temperature shows that the La2O3 phase was increasing. This was supported by the EDS analysis, which showed that the EDS spectrum contains elements La, Ni, and O where the element O indicates that oxidation occurs in the elements Ni and La. On the other hand, the SEM analysis results confirm that the black powder sample contains the elements La and Ni, based on the high and low electron images contained in the morphology of the black powder sample. In addition, it was also known that the particles in the black powder sample were micron size and had porous morphology. This occurs due to rapid thermal decomposition events and excessive gas development. In addition, FTIR analysis showed that the O-H bond had been reduced and there are still C-O and C-H bonds indicating the presence of organic elements possessed by glycine.

Controlling the Velocity and Kinetic Energy of an Ideal Gas: An EWMA Control Chart and Its Average Run Length

An ideal gas is a gas in the form of a particle or molecule. Its velocity and kinetic energy are interesting topics in several studies in physical chemistry. This research aims to evaluate the average run length based on the exponentially weighted moving average statistic for its molecular velocity and kinetic energy of Maxwell-Boltzmann distribution. Derivation of the integral equation, which is equal to the average run length and numerical method of the integral equation, was applied to evaluate the average run length of a gas molecule’s molecular velocity and kinetic energy. The Trapezoidal rule as numerical method and its error was analyzed for approximation of average run length. The findings showed that the average run length of molecular velocity decreased in the higher temperature with the given mass of the molecule. Moreover, there was a decrease in the average run length of molecular kinetic energy in the higher temperature.

STUDY OF ANALYTICAL CHEMISTRY IN MODERN CONDITIONS

The article considers the problems that arise when studying analytical chemistry by students, identifies forms, methods and tools that help to effectively develop and assimilate new knowledge by graduates. Priority educational technologies are presented, which do not provide ready-made knowledge, but encourage search, and in which the role of the teacher is reduced to the function of tutor and organizer, which helps to increase student self-esteem, lays the foundations of his professional growth. The objective of the article is to determine scientifically grounded approaches and choose effective forms, methods and means of the development of professional competence of students studying Analytical Chemistry. The course of analytical chemistry forms the basic practical skills that will be needed by the student during the study of organic, pharmaceutical, toxicological, physical and biological chemistry and involves the formation of skills to apply the acquired knowledge to study special disciplines and professional activities. As a subject, analytical chemistry remains a complex but vital part of the curriculum, in which students are taught to understand the principles by which analytical methods work, as well as to interpret the quantitative data obtained.. That is why it is so important that students not only gain theoretical knowledge, but also understand the nature of the considered techniques, as well as their relative advantages and applications. It is now common practice to include a variety of formats in laboratory manuals for ease of use, but diagrams have been and remain useful, especially in terms of equipment setup, experimental design, and analytical techniques. Communication with students while studying Analytical Chemistry has a positive effect on learning. Changes in the teaching method, namely the use of video during lectures, which explain the basics of methods, presentations with space for notes, platforms where students can ask questions to the teacher, improve the level of mastery of the material. The most effective means of developing professional skills in students of higher educational institutions are laboratory projects, i.e. joint solution of practical problems.

Dewatering Green Sapwood Using Carbon Dioxide Undergoing Cyclical Phase Change between Supercritical Fluid and Gas.

Conventional kiln drying of wood operates by the evaporation of water at elevated temperature. In the initial stage of drying, mobile water in the wood cell lumen evaporates. More slowly, water bound in the wood cell walls evaporates, requiring the breaking of hydrogen bonds between water molecules and cellulose and hemicellulose polymers in the cell wall. An alternative for wood kiln drying is a patented process for green wood dewatering through the molecular interaction of supercritical carbon dioxide with water of wood cell sap. When the system pressure is reduced to below the critical point, phase change from supercritical fluid to gas occurs with a consequent large change in CO2 volume. This results in the efficient, rapid, mechanical expulsion of liquid sap from wood. The end-point of this cyclical phase-change process is wood dewatered to the cell wall fibre saturation point. This paper describes dewatering over a range of green wood specimen sizes, from laboratory physical chemistry studies to pilot-plant trials. Magnetic resonance imaging and nuclear magnetic resonance spectroscopy were applied to study the fundamental mechanisms of the process, which were contrasted with similar studies of conventional thermal wood drying. In conclusion, opportunities and impediments towards the commercialisation of the green wood dewatering process are discussed.

Happy Birthday to Bernd Giese

Happy Birthday to Bernd Giese

Constructing a simple electrolyte conductivity meter for chemistry learning

This research is based on the idea of the need for an innovative experimental learning media in the study of physical chemistry on electrolyte solutions conductivity concept. Through Research and Development method with the stages of analysis, design and development, a simple electrolyte conductivity measurement device has been produced. Based on the results of the research, the product was obtained in the form of an electrolyte solution conductivity measuring device that equipped with a user guidebook and an experimental worksheet of the electrolyte solution conductivity measurement. The electrolyte solution conductivity device is designed to measure the conductivity of an electrolyte solution. This measurement device is able to compare the conductivity value of fruit juices, vegetable juices and isotonic drinks quantitatively based on Kohlrausch’s law with simple and easy devices and materials. The validation result shows that the product is valid. The product was tested to chemistry education students using a feasibility test instrument. The result shows that the average of the value of the feasibility test is 93.85%. These results indicate that the constructed electrolyte conductivity meter is feasible to be used.

Experienced difficulties of BSE-Chemistry students in physical chemistry and suggested enhancement

This study aimed to determine the experienced difficulties in Chemistry 70 (Introduction to Physical Chemistry) among ten (10) selected BSE-Chemistry students who had undergone Chemistry 70 and two professors of Physical Chemistry. Qualitative research design with purposive sampling was used in this study. It was found that out of the total 10 BSE-Chemistry respondents, majority got a passing grade of 1.50 to 3.00 in Chemistry 70, representing their academic performance for this particular study. They considered “Chemical Thermodynamics and Equilibrium” as “much difficult” and classified “teacher factor” as the primary reason for the difficulty in understanding the subject. Teachers play a great role in the learning of the students in Physical Chemistry. They must be equipped effectively with the concepts needed for the efficient delivery of lessons in the classroom. Moreover, teachers must be able to relate both theories and concepts to real-life situations for the students to have a better understanding of the subject matter. It was suggested that students should be able to master the basic skills and concepts in Math 61 to improve their mathematical skills which are very much needed in the study of Physical Chemistry.

The Evaluation of Poly(imide) Siloxane to use in Biomedical and Radiotherapy Applications

Poly(imide) siloxane encourages new research studies that offer innovative and comprehensive industrial areas, experimental approaches and their innovative products. Poly(imide) siloxane covers the studies in fundamental organic polymer chemistry and physical organic chemistry, noval researches on membranes and interfaces. The possible applications of the poly(imide) siloxane as shielding material include facilities such as biological shielding at nuclear medicine departments.

Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations.

The native chemical ligation reaction (NCL) involves reacting a C-terminal peptide thioester with an N-terminal cysteinyl peptide to produce a native peptide bond between the two fragments. This reaction has considerably extended the size of polypeptides and proteins that can be produced by total synthesis and has also numerous applications in bioconjugation, polymer synthesis, material science, and micro- and nanotechnology research. The aim of the present review is to provide a thorough mechanistic overview of NCL and extended methods. The most relevant properties of peptide thioesters, Cys peptides, and common solvents, reagents, additives, and catalysts used for these ligations are presented. Mechanisms, selectivity and reactivity are, whenever possible, discussed through the insights of computational and physical chemistry studies. The inherent limitations of NCL are discussed with insights from the mechanistic standpoint. This review also presents a palette of O, S-, N, S-, or N, Se-acyl shift systems as thioester or selenoester surrogates and discusses the special molecular features that govern reactivity in each case. Finally, the various thiol-based auxiliaries and thiol or selenol amino acid surrogates that have been developed so far are discussed with a special focus on the mechanism of long-range N, S-acyl migrations and selective dechalcogenation reactions.

Physical Chemistry of Cellular Liquid-Phase Separation.

Compartmentalization of biochemical processes is essential for cell function. Although membrane-bound organelles are well studied in this context, recent work has shown that phase separation is a key contributor to cellular compartmentalization through the formation of liquid-like membraneless organelles (MLOs). In this Minireview, the key mechanistic concepts that underlie MLO dynamics and function are first briefly discussed, including the relevant noncovalent interaction chemistry and polymer physical chemistry. Next, a few examples of MLOs and relevant proteins are given, along with their functions, which highlight the relevance of the above concepts. The developing area of active matter and non-equilibrium systems, which can give rise to unexpected effects in fluctuating cellular conditions, are also discussed. Finally, our thoughts for emerging and future directions in the field are discussed, including in vitro and in vivo studies of MLO physical chemistry and function.

Molecular simulations for the spectroscopic detection of atmospheric gases.

Unambiguously identifying molecules in spectra is of fundamental importance for a variety of scientific and industrial uses. Interpreting atmospheric spectra for the remote detection of volatile compounds requires information about the spectrum of each relevant molecule. However, spectral data currently exist for a few hundred molecules and only a fraction of those have complete spectra (e.g. H2O, NH3). Consequently, molecular detections in atmospheric spectra remain vulnerable to false positives, false negatives, and missassignments. There is a key need for spectral data for a broad range of molecules. Given how challenging it is to obtain high-resolution molecular spectra, there is great value in creating intermediate approximate spectra that can provide a starting point for the analysis of atmospheric spectra. Using a combination of experimental measurements, organic chemistry, and quantum mechanics, RASCALL (Rapid Approximate Spectral Calculations for ALL) is a computational approach that provides approximate spectral data for any given molecule, including thousands of potential atmospheric gases. RASCALL is a new theoretical chemistry method for the simulation of spectral data. RASCALL 1.0, presented here, is capable of simulating molecular spectral data, in a few seconds, by interpreting functional group data from experimental and theoretical sources to estimate the position and strength of molecular bands. The RASCALL 1.0 spectra consist of approximate band centers and qualitative intensities. RASCALL 1.0 is also able to assess hundreds of molecules simultaneously, which will inform prioritization protocols for future, computationally and experimentally costly, high-accuracy physical chemistry studies. Finally, RASCALL can be used to study spectral patterns between molecules, highlighting ambiguities in molecular detections and also directing observations towards spectral regions that reduce the degeneracy in molecular identification. The RASCALL catalogue, and its preliminary version RASCALL 1.0, contains spectral data for more molecules than any other publicly available database, with applications in all fields interested in the detection of molecules in the gas phase (e.g., medical imaging, petroleum industry, pollution monitoring, astrochemistry). The preliminary catalogue of molecular data and associated documentation are freely available online and will be routinely updated.

Сравнительные исследования эффективности антиокислителей

Due to their role in preserving the quality and safety of food products having a long shelf life, a study into the effectiveness of food additives with antimicrobial properties appears to be an urgent task. The purpose of the present work is to carry out a comparative assessment of the antioxidant activity of ascorbyl palmitate, alpha-tocopherol, lecithin and dihydroquercetin (taxifolin). Antioxidants were added to a sample of chopped pork fat. After the introduction of the antioxidant, the raw fat was packaged in polymer bags. Then, the sampled raw fat was stored at a temperature of 4±2 °С for 12 days. During the entire shelf life (0, 4, 6, 12 days), studies were conducted to determine the organoleptic characteristics and indicators of hydrolytic (acid number) and oxidative deterioration (peroxide and thiobarbituric number). The organoleptic test on the 6th day revealed the appearance of a yellowish tint in the raw fat admixed with ascorbyl palmitate and lecithin. Moreover, all samples corresponded to the established normalised oxidative deterioration indicator values for the 6-day period. By the end of the storage period (12 days), the samples, with exception of those prepared with the addition of alpha-tocopherol and dihydroquercetin, had a noticeable odour and greenish tinge. Obtained data agreed with the results of physical chemistry studies. Over the period of 6 days of storage, a significant increase was observed in the indices of oxiditative deterioration in all pork fat samples with exception of those admixed with alpha-tocopherol and dihydroquercetin. The most effective action of tocopherol and digidrokvertsetin was applied to the reduction in the accumulation of the second fat oxidation products, which was expressed in a reduction in the thiobarbituric number on the 12th day of storage by 37% and 70%, respectively, in comparison with the control samples. On the basis of the experimental results, it can be concluded that alpha-tocopherol and dihydroquercetin are effective antioxidants for the preservation of animal fat.

Heterolytic (2 e) vs Homolytic (1 e) Oxidation Reactivity: N-H versus C-H Switch in the Oxidation of Lactams by Dioxirans.

Dioxiranes are powerful oxidants that can act via two different mechanisms: 1) homolytic (H abstraction and oxygen rebound) and 2) heterolytic (electrophilic oxidation). So far, it has been reported that the nature of the substrate dictates the reaction mode independently from the dioxirane employed. Herein, we report an unprecedented case in which the nature of the dioxirane rules the oxidation chemoselectivity. In particular, a switch from C-H to N-H oxidation is observed in the oxidation of lactams moving from dimethyl dioxirane (DDO) to methyl(trifluoromethyl)dioxirane (TFDO). A physical organic chemistry study, which combines the oxidation with two other dioxiranes methyl(fluoromethyl)dioxirane, MFDO, and methyl(difluoromethyl)dioxirane, DFDO, with computational studies, points to a diverse ability of the dioxiranes to either stabilize the homo or the heterolytic pathway.

Robust magnetic moments on the basal plane of the graphene sheet effectively induced by OH groups.

Inducing robust magnetic moments on the basal plane of the graphene sheet is very difficult, and is one of the greatest challenges in the study of physical chemistry of graphene materials. Theoretical studies predicted that introduction of a kind of sp3-type defects formed by OH groups is an effective pathway to achieve this goal [Boukhvalov, D. W. & Katsnelson, M. I. ACS Nano 5, 2440–2446 (2011)]. Here we demonstrate that OH groups can efficiently induce robust magnetic moments on the basal plane of the graphene sheet. We show that the inducing efficiency can reach as high as 217 μB per 1000 OH groups. More interestingly, the magnetic moments are robust and can survive even at 900°C. Our findings highlight the importance of OH group as an effective sp3-type candidate for inducing robust magnetic moments on the basal plane of the graphene sheet.

Microbead analysis of cell binding to immobilized lectin. Part II: Quantitative kinetic profile assay for possible identification of anti-infectivity and anti-cancer reagents

There has been a re-emergence of the use of lectins in a variety of therapeutic venues. In addition lectins are often responsible for the binding of pathogens to cells and for cancer cell clumping that increases their escape from body defenses. It is important to define precisely the activity of inhibitors of lectin-binding that may be used in anti-infection and anti-cancer therapeutics. Here we describe a kinetic assay that measures the activity of saccharide inhibitors of lectin binding using a model system of yeast (Saccharomyces cerevisiae) and lectin (Concanavalin A, Con A) derivatized agarose microbeads that mimics pathogen-cell binding. We show that old methods (part I of this study) used to identify inhibitor activity using only one sugar concentration at one time point can easily provide wrong information about inhibitor activity. We assess the activity of 4 concentrations of 10 saccharides at 4 different times in 400 trials and statistically evaluate the results. We show that d-melezitose is the best inhibitor of yeast binding to the lectin microbeads. These results, along with physical chemistry studies, provide a solid foundation for the development of drugs that may be useful in anti-infectivity and anti-cancer therapeutics.