The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol operates on a wide variety of platforms. For example, Jmol is functional in Mozilla Firefox, Internet Explorer, Google Chrome, Safari. Chemistry Development Kit Comparison of software for molecular mechanics modeling Jmol extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule editor Proteopedia PyMOL SAMSON Official website Wiki with listings of websites and moodles Willighagen, Egon. "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D". Doi:10.1038/npre.2007.50.1
The melting point of a substance is the temperature at which it changes state from solid to liquid. At the melting point the solid and liquid phase exist in equilibrium; the melting point of a substance depends on pressure and is specified at a standard pressure such as 1 atmosphere or 100 kPa. When considered as the temperature of the reverse change from liquid to solid, it is referred to as the freezing point or crystallization point; because of the ability of some substances to supercool, the freezing point is not considered as a characteristic property of a substance. When the "characteristic freezing point" of a substance is determined, in fact the actual methodology is always "the principle of observing the disappearance rather than the formation of ice", that is, the melting point. For most substances and freezing points are equal. For example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures.
For example, agar melts at 85 °C and solidifies from 31 °C. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances, the freezing point of water is not always the same as the melting point. In the absence of nucleators water can exist as a supercooled liquid down to −48.3 °C before freezing. The chemical element with the highest melting point is tungsten, at 3,414 °C; the often-cited carbon does not melt at ambient pressure but sublimes at about 3,726.85 °C. Tantalum hafnium carbide is a refractory compound with a high melting point of 4215 K. At the other end of the scale, helium does not freeze at all at normal pressure at temperatures arbitrarily close to absolute zero. Many laboratory techniques exist for the determination of melting points. A Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip, revealing its thermal behaviour at the temperature at that point. Differential scanning calorimetry gives information on melting point together with its enthalpy of fusion.
A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window and a simple magnifier. The several grains of a solid are placed in a thin glass tube and immersed in the oil bath; the oil bath is heated and with the aid of the magnifier melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, optical detection is automated; the measurement can be made continuously with an operating process. For instance, oil refineries measure the freeze point of diesel fuel online, meaning that the sample is taken from the process and measured automatically; this allows for more frequent measurements as the sample does not have to be manually collected and taken to a remote laboratory. For refractory materials the high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees.
The spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source, calibrated as a function of temperature. In this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer. For temperatures above the calibration range of the source, an extrapolation technique must be employed; this extrapolation is accomplished by using Planck's law of radiation. The constants in this equation are not known with sufficient accuracy, causing errors in the extrapolation to become larger at higher temperatures. However, standard techniques have been developed to perform this extrapolation. Consider the case of using gold as the source. In this technique, the current through the filament of the pyrometer is adjusted until the light intensity of the filament matches that of a black-body at the melting point of gold.
This establishes the primary calibration temperature and can be expressed in terms of current through the pyrometer lamp. With the same current setting, the pyrometer is sighted on another black-body at a higher temperature. An absorbing medium of known transmission is inserted between this black-body; the temperature of the black-body is adjusted until a match exists between its intensity and that of the pyrometer filament. The true higher temperature of the black-body is determined from Planck's Law; the absorbing medium is removed and the current through the filament is adjusted to match the filament intensity to that of the black-body. This establishes a second calibration point for the pyrometer; this step is repeated to carry the calibration to hi
The boiling point of a substance is the temperature at which the vapor pressure of a liquid equals the pressure surrounding the liquid and the liquid changes into a vapor. The boiling point of a liquid varies depending upon the surrounding environmental pressure. A liquid in a partial vacuum has a lower boiling point than when that liquid is at atmospheric pressure. A liquid at high pressure has a higher boiling point than when that liquid is at atmospheric pressure. For example, water at 93.4 °C at 1,905 metres altitude. For a given pressure, different liquids will boil at different temperatures; the normal boiling point of a liquid is the special case in which the vapor pressure of the liquid equals the defined atmospheric pressure at sea level, 1 atmosphere. At that temperature, the vapor pressure of the liquid becomes sufficient to overcome atmospheric pressure and allow bubbles of vapor to form inside the bulk of the liquid; the standard boiling point has been defined by IUPAC since 1982 as the temperature at which boiling occurs under a pressure of 1 bar.
The heat of vaporization is the energy required to transform a given quantity of a substance from a liquid into a gas at a given pressure. Liquids may change to a vapor at temperatures below their boiling points through the process of evaporation. Evaporation is a surface phenomenon in which molecules located near the liquid's edge, not contained by enough liquid pressure on that side, escape into the surroundings as vapor. On the other hand, boiling is a process in which molecules anywhere in the liquid escape, resulting in the formation of vapor bubbles within the liquid. A saturated liquid contains as much thermal energy. Saturation temperature means boiling point; the saturation temperature is the temperature for a corresponding saturation pressure at which a liquid boils into its vapor phase. The liquid can be said to be saturated with thermal energy. Any addition of thermal energy results in a phase transition. If the pressure in a system remains constant, a vapor at saturation temperature will begin to condense into its liquid phase as thermal energy is removed.
A liquid at saturation temperature and pressure will boil into its vapor phase as additional thermal energy is applied. The boiling point corresponds to the temperature at which the vapor pressure of the liquid equals the surrounding environmental pressure. Thus, the boiling point is dependent on the pressure. Boiling points may be published with respect to the NIST, USA standard pressure of 101.325 kPa, or the IUPAC standard pressure of 100.000 kPa. At higher elevations, where the atmospheric pressure is much lower, the boiling point is lower; the boiling point increases with increased pressure up to the critical point, where the gas and liquid properties become identical. The boiling point cannot be increased beyond the critical point; the boiling point decreases with decreasing pressure until the triple point is reached. The boiling point cannot be reduced below the triple point. If the heat of vaporization and the vapor pressure of a liquid at a certain temperature are known, the boiling point can be calculated by using the Clausius–Clapeyron equation, thus: T B = − 1, where: T B is the boiling point at the pressure of interest, R is the ideal gas constant, P is the vapour pressure of the liquid at the pressure of interest, P 0 is some pressure where the corresponding T 0 is known, Δ H vap is the heat of vaporization of the liquid, T 0 is the boiling temperature, ln is the natural logarithm.
Saturation pressure is the pressure for a corresponding saturation temperature at which a liquid boils into its vapor phase. Saturation pressure and saturation temperature have a direct relationship: as saturation pressure is increased, so is saturation temperature. If the temperature in a system remains constant, vapor at saturation pressure and temperature will begin to condense into its liquid phase as the system pressure is increased. A liquid at saturation pressure and temperature will tend to flash into its vapor phase as system pressure is decreased. There are two conventions regarding the standard boiling point of water: The normal boiling point is 99.97 °C at a pressure of 1 atm. The IUPAC recommended standard boiling point of water at a standard pressure of 100 kPa is 99.61 °C. For comparison, on top of Mount Everest, at 8,848 m elevation, the pressure is about 34 kPa and the boiling point of water is 71 °C; the Celsius temperature scale was defined until 1954 by two points: 0 °C being defined by the wate
European Chemicals Agency
The European Chemicals Agency is an agency of the European Union which manages the technical and administrative aspects of the implementation of the European Union regulation called Registration, Evaluation and Restriction of Chemicals. ECHA is the driving force among regulatory authorities in implementing the EU's chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and addresses chemicals of concern, it is located in Finland. The agency headed by Executive Director Bjorn Hansen, started working on 1 June 2007; the REACH Regulation requires companies to provide information on the hazards and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most used substances have been registered; the information is technical but gives detail on the impact of each chemical on people and the environment.
This gives European consumers the right to ask retailers whether the goods they buy contain dangerous substances. The Classification and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU; this worldwide system makes it easier for workers and consumers to know the effects of chemicals and how to use products safely because the labels on products are now the same throughout the world. Companies need to notify ECHA of the labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100 000 substances; the information is available on their website. Consumers can check chemicals in the products. Biocidal products include, for example, insect disinfectants used in hospitals; the Biocidal Products Regulation ensures that there is enough information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation; the law on Prior Informed Consent sets guidelines for the import of hazardous chemicals.
Through this mechanism, countries due to receive hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have serious effects on human health and the environment are identified as Substances of Very High Concern 1; these are substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment and do not break down. Other substances considered. Companies manufacturing or importing articles containing these substances in a concentration above 0,1% weight of the article, have legal obligations, they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy. Once a substance has been identified in the EU as being of high concern, it will be added to a list; this list is available on ECHA's website and shows consumers and industry which chemicals are identified as SVHCs.
Substances placed on the Candidate List can move to another list. This means that, after a given date, companies will not be allowed to place the substance on the market or to use it, unless they have been given prior authorisation to do so by ECHA. One of the main aims of this listing process is to phase out SVHCs where possible. In its 2018 substance evaluation progress report, ECHA said chemical companies failed to provide “important safety information” in nearly three quarters of cases checked that year. "The numbers show a similar picture to previous years" the report said. The agency noted that member states need to develop risk management measures to control unsafe commercial use of chemicals in 71% of the substances checked. Executive Director Bjorn Hansen called non-compliance with REACH a "worry". Industry group CEFIC acknowledged the problem; the European Environmental Bureau called for faster enforcement to minimise chemical exposure. European Chemicals Bureau Official website
ArXiv is a repository of electronic preprints approved for posting after moderation, but not full peer review. It consists of scientific papers in the fields of mathematics, astronomy, electrical engineering, computer science, quantitative biology, mathematical finance and economics, which can be accessed online. In many fields of mathematics and physics all scientific papers are self-archived on the arXiv repository. Begun on August 14, 1991, arXiv.org passed the half-million-article milestone on October 3, 2008, had hit a million by the end of 2014. By October 2016 the submission rate had grown to more than 10,000 per month. ArXiv was made possible by the compact TeX file format, which allowed scientific papers to be transmitted over the Internet and rendered client-side. Around 1990, Joanne Cohn began emailing physics preprints to colleagues as TeX files, but the number of papers being sent soon filled mailboxes to capacity. Paul Ginsparg recognized the need for central storage, in August 1991 he created a central repository mailbox stored at the Los Alamos National Laboratory which could be accessed from any computer.
Additional modes of access were soon added: FTP in 1991, Gopher in 1992, the World Wide Web in 1993. The term e-print was adopted to describe the articles, it began as a physics archive, called the LANL preprint archive, but soon expanded to include astronomy, computer science, quantitative biology and, most statistics. Its original domain name was xxx.lanl.gov. Due to LANL's lack of interest in the expanding technology, in 2001 Ginsparg changed institutions to Cornell University and changed the name of the repository to arXiv.org. It is now hosted principally with eight mirrors around the world, its existence was one of the precipitating factors that led to the current movement in scientific publishing known as open access. Mathematicians and scientists upload their papers to arXiv.org for worldwide access and sometimes for reviews before they are published in peer-reviewed journals. Ginsparg was awarded a MacArthur Fellowship in 2002 for his establishment of arXiv; the annual budget for arXiv is $826,000 for 2013 to 2017, funded jointly by Cornell University Library, the Simons Foundation and annual fee income from member institutions.
This model arose in 2010, when Cornell sought to broaden the financial funding of the project by asking institutions to make annual voluntary contributions based on the amount of download usage by each institution. Each member institution pledges a five-year funding commitment to support arXiv. Based on institutional usage ranking, the annual fees are set in four tiers from $1,000 to $4,400. Cornell's goal is to raise at least $504,000 per year through membership fees generated by 220 institutions. In September 2011, Cornell University Library took overall administrative and financial responsibility for arXiv's operation and development. Ginsparg was quoted in the Chronicle of Higher Education as saying it "was supposed to be a three-hour tour, not a life sentence". However, Ginsparg remains on the arXiv Scientific Advisory Board and on the arXiv Physics Advisory Committee. Although arXiv is not peer reviewed, a collection of moderators for each area review the submissions; the lists of moderators for many sections of arXiv are publicly available, but moderators for most of the physics sections remain unlisted.
Additionally, an "endorsement" system was introduced in 2004 as part of an effort to ensure content is relevant and of interest to current research in the specified disciplines. Under the system, for categories that use it, an author must be endorsed by an established arXiv author before being allowed to submit papers to those categories. Endorsers are not asked to review the paper for errors, but to check whether the paper is appropriate for the intended subject area. New authors from recognized academic institutions receive automatic endorsement, which in practice means that they do not need to deal with the endorsement system at all. However, the endorsement system has attracted criticism for restricting scientific inquiry. A majority of the e-prints are submitted to journals for publication, but some work, including some influential papers, remain purely as e-prints and are never published in a peer-reviewed journal. A well-known example of the latter is an outline of a proof of Thurston's geometrization conjecture, including the Poincaré conjecture as a particular case, uploaded by Grigori Perelman in November 2002.
Perelman appears content to forgo the traditional peer-reviewed journal process, stating: "If anybody is interested in my way of solving the problem, it's all there – let them go and read about it". Despite this non-traditional method of publication, other mathematicians recognized this work by offering the Fields Medal and Clay Mathematics Millennium Prizes to Perelman, both of which he refused. Papers can be submitted in any of several formats, including LaTeX, PDF printed from a word processor other than TeX or LaTeX; the submission is rejected by the arXiv software if generating the final PDF file fails, if any image file is too large, or if the total size of the submission is too large. ArXiv now allows one to store and modify an incomplete submission, only finalize the submission when ready; the time stamp on the article is set. The standard access route is through one of several mirrors. Sev
Acid dissociation constant
An acid dissociation constant, Ka, is a quantitative measure of the strength of an acid in solution. It is the equilibrium constant for a chemical reaction known as dissociation in the context of acid–base reactions. K a =; the chemical species HA, A−, H+ are said to be in equilibrium when their concentrations do not change with the passing of time, because both forward and backward reactions are occurring at the same fast rate. The chemical equation for acid dissociation can be written symbolically as: HA ↽ − − ⇀ A − + H + where HA is a generic acid that dissociates into A−, the conjugate base of the acid and a hydrogen ion, H+, it is implicit in this definition that the quotient of activity coefficients, Γ, Γ = γ A − γ H + γ A H is a constant that can be ignored in a given set of experimental conditions. For many practical purposes it is more convenient to discuss the logarithmic constant, pKa p K a = − log 10 The more positive the value of pKa, the smaller the extent of dissociation at any given pH —that is, the weaker the acid.
A weak acid has a pKa value in the approximate range −2 to 12 in water. For a buffer solution consisting of a weak acid and its conjugate base, pKa can be expressed as: p K a = pH − log 10 The pKa for a weak monoprotic acid is conveniently determined by potentiometric titration with a strong base to the equivalence point and taking the pH value measured at one-half this volume as being equal to pKa; that is because at this half equivalence point, the number of moles of strong base added is one-half the number of moles of weak acid present, while the concentrations of the conjugate base and the remaining weak acid are the same. Acids with a pKa value of less than about −2 are said to be strong acids. In water, the dissociation of a strong acid in dilute solutions is complete such that the final concentration of the undissociated acid final is low. Consider a strong monoprotic acid, such as HCl; because of their 1:1 ratio, the final concentration of the conjugate base, final, is taken to be equal to the concentration of the hydronium ion, which can be directly measured by a pH meter.
For strong monoprotic acids like HCl, final and are both nearly equal to the initial concentration of initial placed into solution. With conventional acid-base titration methods it is difficult to measure the pH of a strong acid solution and, hence, to determine the or final, with a sufficient number of significant figures to and compute the low values encountered for final, which can be as low as 10-9 mol per liter for some strong acids. Furthermore, if 100% dissociation is assumed, final is zero and the fraction within parenthesis in the equation above becomes undefined; because the second expression on the right-hand side of the above equation is therefore indeterminable by conventional titration methods, the entire equation is not as useful a means of experimentally measuring pKa for strong acids as it is for weak acids. However, pKa and/or Ka values for strong acids can be estimated by theoretical means, such as computing gas phase dissociation constants and using Gibbs free energies of solvation for the molecular anions.
It is possible to use spectroscopy in some cases to determine the ratio of the concentrations of the conjugate base produced and the undissociated acid. For example, the Raman spectra of dilute nitric acid solutions contain signals of the nitrate ion and as the solutions become more concentrated signals of undissociated nitric acid molecules emerge; the acid dissociation constant for an acid is a direct consequence of the underlying thermodynamics of the dissociation reaction. The value of the pKa changes with temperature and can be understood qualitatively based on Le Châtelier's principle: when the reaction is endothermic, Ka increases and pKa decreases with
In the physical sciences, a partition coefficient or distribution coefficient is the ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium. This ratio is therefore a measure of the difference in solubility of the compound in these two phases; the partition coefficient refers to the concentration ratio of un-ionized species of compound, whereas the distribution coefficient refers to the concentration ratio of all species of the compound. In the chemical and pharmaceutical sciences, both phases are solvents. Most one of the solvents is water, while the second is hydrophobic, such as 1-octanol. Hence the partition coefficient measures how hydrophobic a chemical substance is. Partition coefficients are useful in estimating the distribution of drugs within the body. Hydrophobic drugs with high octanol/water partition coefficients are distributed to hydrophobic areas such as lipid bilayers of cells. Conversely, hydrophilic drugs are found in aqueous regions such as blood serum.
If one of the solvents is a gas and the other a liquid, a gas/liquid partition coefficient can be determined. For example, the blood/gas partition coefficient of a general anesthetic measures how the anesthetic passes from gas to blood. Partition coefficients can be defined when one of the phases is solid, for instance, when one phase is a molten metal and the second is a solid metal, or when both phases are solids; the partitioning of a substance into a solid results in a solid solution. Partition coefficients can be measured experimentally in various ways or estimated by calculation based on a variety of methods. Despite formal recommendation to the contrary, the term partition coefficient remains the predominantly used term in the scientific literature. In contrast, the IUPAC recommends that the title term no longer be used, that it be replaced with more specific terms. For example, partition constant, defined as where KD is the process equilibrium constant, represents the concentration of solute A being tested, "org" and "aq" refer to the organic and aqueous phases respectively.
The IUPAC further recommends "partition ratio" for cases where transfer activity coefficients can be determined, "distribution ratio" for the ratio of total analytical concentrations of a solute between phases, regardless of chemical form. The partition coefficient, abbreviated P, is defined as a particular ratio of the concentrations of a solute between the two solvents for un-ionized solutes, the logarithm of the ratio is thus log P; when one of the solvents is water and the other is a non-polar solvent the log P value is a measure of lipophilicity or hydrophobicity. The defined precedent is for the lipophilic and hydrophilic phase types to always be in the numerator and denominator respectively. To a first approximation, the non-polar phase in such experiments is dominated by the un-ionized form of the solute, electrically neutral, though this may not be true for the aqueous phase. To measure the partition coefficient of ionizable solutes, the pH of the aqueous phase is adjusted such that the predominant form of the compound in solution is the un-ionized, or its measurement at another pH of interest requires consideration of all species, un-ionized and ionized.
A corresponding partition coefficient for ionizable compounds, abbreviated log P I, is derived for cases where there are dominant ionized forms of the molecule, such that one must consider partition of all forms, ionized and un-ionized, between the two phases. M is used to indicate the number of ionized forms. For instance, for an octanol–water partition, it is log P oct/wat I = log . To distinguish between this and the standard, un-ionized, partition coefficient, the un-ionized is assigned the symbol log P0, such that the indexed log P oct/wat I expression for ionized solutes becomes an extension of this, into the range of values I > 0. The distribution co