Merge pull request #1 from virtual-labs/testing

Testing

experiment-descriptor.json

@@ -0,0 +1,46 @@
+{
+  "unit-type": "lu",
+  "label": "",
+  "basedir": ".",
+  "units": [
+    {
+      "unit-type": "aim"
+    },
+    {
+      "target": "theory.html",
+      "source": "theory.md",
+      "label": "Theory",
+      "unit-type": "task",
+      "content-type": "text"
+    },
+    {
+      "target": "objective.html",
+      "source": "objective.md",
+      "label": "Objective",
+      "unit-type": "task",
+      "content-type": "text"
+    },
+    {
+      "target": "simulation.html",
+      "source": "simulation/index.html",
+      "label": "Simulation",
+      "unit-type": "task",
+      "content-type": "simulation"
+    },
+    {
+      "target": "assignment.html",
+      "source": "assignment.md",
+      "label": "Assignment",
+      "unit-type": "task",
+      "content-type": "text"
+    },
+    {
+      "target": "references.html",
+      "source": "references.md",
+      "label": "References",
+      "unit-type": "task",
+      "content-type": "text"
+    }
+  ]
+}
+

experiment/aim.md

@@ -1 +1,3 @@
-### Aim of the experiment
+A molecule upon interacting with incident light may scatter a part of the light ( elastically, e.g., Rayleigh scattering or inelastically, e.g., Raman scattering) and may absorb rest of the light. An absorption of light may occur when the photon energy is equal to the energy difference between two energy states of the molecule. The interaction of the oscillating electromagnetic field of the radiation with the charged particles (electrons) in the molecule causes absorption of light. The absorption of light energy places the molecule in one of its many possible higher energy (excited) rotational, vibrational or electronic states, depending on the amount of the absorbed energy. Thus the molecule undergoes a transition to an upper energy or excited state. This is known as excitation or absorption process. The absorption process is extremely fast (takes approx. 10-15 s). All electronically excited states have a finite lifetime during which the excited state equilibrates with its surroundings. Therefore, after reaching the excited electronic state, the molecule returns to its ground state by losing the absorbed energy via various pathways that are either radiationless, in which no photons are emitted (energy converted into the disordered thermal motion of its surroundings), or radiative decay, which involves the emission of a photon. For example, the molecule can lose the energy by internal conversion (heat), quenching (external conversion), by emission of a photon (fluorescence), or by first intersystem crossing and then emission of a photon (phosphorescence). A schematic of the processes that occur following the electronic transition is given by `Jablonski diagram` after Polish physicist, Aleksander Jablonski.
+
+

experiment/assignment.md

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+**Q1**. How many possible orientations can two parallel spins adopt with respect to the external magnetic field? Show by schematic diagram.
+
+**Q2**. What are the spin multiplicity and the spin of triplet state?
+
+**Q3**. Why two electrons are always present in two different orbitals of the molecule in triplet state?
+
+**Q4**. Internal conversion (takes place at a time scale of 10-12 s) is faster than the fluorescence emission. Then how does radiative emission (fluorescence) compete with the non-radiative transition? (Hint: Significantly larger energy gap between S1 and S0 and longer lifetime of S1.)
+
+**Q5**. Transitions between states of different multiplicity are formally forbidden. What are the mechanisms that make the intersystem crossing probable?
+
+**Q6**. How can you justify that the relaxation to ground state occurs via 'vertical' transition?
+
+**Q7**. In most of the cases, the S1 potential energy curve shifts to the right with respect to S0 potential energy curve. Justify it. (Hint: In the excited state, the electron is promoted to an anti-bonding orbital.)
+
+**Q8**. Why are absorption and fluorescence much faster than phosphorescence?

experiment/experiment-name.md

@@ -1 +1 @@
-## Experiment name
+## Introduction to the fluorescence spectroscopy principle

experiment/objective.md

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+- To be introduced to the principles of fluorescence (and phosphorescence) in a molecule 

experiment/procedure.md

@@ -1 +1 @@
-### Procedure
+Procedure is under construction.

experiment/references.md

@@ -1 +1,7 @@
-### Link your references in here
+1. B. Valeur , Molecular Fluorescence : Principles and Applications , 2002, Wiley-VCH, Weinheim.  
+2. J. R. Albani , Principles and Applications of Fluorescence Spectroscopy, 2007, Blackwell Science Science Ltd, Oxford, UK.  
+3. P. Patnaik, Dean's Analytical Chemistry Handbook, 2nd Edition, McGraw-Hill Handbooks.  
+4. Frank A. Settle, Handbook of Instrumental Techniques for Analytical Chemistry, 1st. Edition, 1997, National Science Foundation, Arlington, Virginia.  
+5. J. R. Lakowicz, Principles of Fluorescence Spectroscopy, 2nd Ed., Kluwer Academic/Plenum Publishers, New York, London, Moscow, Dordrecht, 1999.  
+6. D. M. Jameson et al. in Basic Concepts in Fluorescence, Fluorescence: Basic Concepts, Principles Aspects and some Anecdotes, Methods Enzymol. 2003, 360, 1.  
+7. P. Atkins and J. D. Paula, Atkin's Physical Chemistry, 9th Edition, Oxford University Press.

experiment/simulation/index.html

@@ -6,7 +6,9 @@
 </head>
 <body>
 		<!-- Your code goes here-->
-
+
+	<p>Click <a href="mfs_exp1.html">here</a> for the Virtual lab on introduction to the fluorescence spectroscopy principle Experiment
+			 </p>
 	<!-- Add JS at the bottom of HTML file --> 
         <script src="./js/main.js"></script>
 </body>

experiment/simulation/mfs_exp1.html

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+<!DOCTYPE html>
+<html>
+<head>
+
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <link rel="stylesheet" href="../../libraries/bootstrap-3.3.7-dist/css/bootstrap.min.css">
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>
+    <script src="../../libraries/bootstrap-3.3.7-dist/js/bootstrap.min.js"></script>
+    <script type="text/javascript">
+        function playVideo(Id) {
+            document.getElementById(Id).play();
+        }
+    </script>
+
+    <style type="text/css">
+        h3{
+            text-align: center;
+            font-weight: bold;
+            font-family:"Times New Roman", Times, serif;
+        }
+        button{
+            margin:auto;
+            display:block;
+        }
+    </style>
+    <title>Florescence Principle</title>
+
+</head>
+<body >
+<div class = "container">
+    <div class= "row">
+        <div class="col-sm-12">
+            <h3>Principle of Absorption, Florescence and Phosphorescence</h3><br>
+            <button onclick = "window.location.reload()">Reset Experiment</button><br>
+            <div class="embed-responsive embed-responsive-16by9">
+                <video id="video"  class="embed-responsive-item"><source src="videos/principle.mp4" type="video/mp4"></video>
+            </div><br>
+            <button onclick = "playVideo('video')">Click here to view the Principle</button>
+        </div>
+    </div>
+</div>  
+</body>
+</html>

experiment/theory.md

@@ -1 +1,8 @@
-### Link your theory in here
+#### Singlet-Triplet States
+In an electronic transition, the electronic configuration changes, i.e., one or more electron(s) in the molecule are rearranged in available higher energy orbitals. Depending on the spin orientations of the excited electron in the new orbital, the states are designated as singlet (S) or triplet (T). In the following we discuss about the singlet and triplet electronic states.
+
+Upon light absorption, electronic transitions result from the interaction between electrons and the electric field component of the light. The magnetic contribution to the absorption is negligible compared to the electric contribution because of the speed of electron rotation on itself is very weak compared to the light velocity [Total energy, F = (eE) + (evH /c) , where e, c, v, E, and H are, respectively, the electron charge, light velocity, speed of rotation of the electron on itself, and electric and magnetic components of the light wave]. Thus, a displaced electron preserves the same spin orientation during absorption excitation. Therefore, if the ground state of a molecule is a singlet state then the transition of the electron occurs to an excited singlet state. In other words, singlet to triplet transitions are forbidden, unless it is assisted by some other mechanism (such as spin-orbit couplings). Similarly, the electronic transition from T → S is formally forbidden (from the selection rules point of view). The absorption of light can excite the molecules from lowest energy singlet state S0 to higher energy singlet state S1 and even to S2 if the excitation energy is sufficient.
+
+Fluorescence and Phosphorescence The Franck-Condon principle states that the heavier nuclei do not change their positions during the fast electronic excitation. This results in an initial geometry of the excited state which is usually not the energy minimum geometry. According to the Franck-Condon principle, the molecule will most probably be excited to one of the higher vibrational states of the excited electronic state. The molecule in an excited vibrational energy level loses energy rapidly (in 10-12 s or less) and moves to a lower (and finally to the lowest) vibrational energy level in the same excited electronic state. Once the molecule is in the lowest vibrational level of the excited electronic state, S1, the molecule can return to one of the vibrational states of the ground singlet state, S0 through an emission of photon radiation, called fluorescence, or via other relaxation path ways. In fluorescence, the acquired (absorbed) electronic energy is lost via the emission of a photon while transition occurs from lowest vibrational level of first excited singlet (i.e., v=0 of S1) to one of the vibrational states of the ground singlet state, S0. This radiative process takes about 10-9 second. Most compounds decay by non-radiative processes (such as heat) and are therefore not fluorescent.
+
+If by some mechanisms, intersystem crossing (say, spin forbidden transition S1 → T1) occurs, then a radiative transition T1 to S0, called phosphorescence, may occur. In intersystem crossing, a molecule in the ground vibrational energy level of an excited electronic state passes into a high vibrational energy level of a lower energy electronic state with a different spin state (say, S1 to T1). Intersystem crossing requires a mechanism for converting the paired electron spins (↑↓) of the singlet state to unpaired electron spins (↑↑) of the triplet state. Spin-orbit coupling and vibronic coupling favor intersystem crossing. In spin-orbit coupling, the magnetic field arising from an electron's orbital motion around the nucleus interacts with the spin magnetic moment of the electron which helps in spin reversal or flipping of electron orientation (from ↑↓ to ↑↑). The strength of the orbitally generated magnetic field increases as the nuclear charge increases. The efficiency of this coupling varies with the fourth power of the atomic number. After intersystem crossing, the molecule as usual undergoes vibrational relaxation and moves down the vibrational energy levels of the T1 state by loss of energy in collisions with surrounding molecules. Then the molecule may transit from T1 to S0 by the emission of a photon, called phosphorescence. The forbidden transition of the molecule from T1 to S0 to occur requires a similar mechanism that permitted singlet to triplet intersystem crossing. Typical mean time for phosphorescence (1 millisecond to 10 second) is longer than that for fluorescence.