Draw an atom

Bohr model describes the visual representation of orbiting electrons around the small nucleus. It used different electron shells such as K, L, M, N…so on. These shells hold a specific number of electrons, the electron shell which is closest to the nucleus has less energy and the electron shell which is farthest from the nucleus has more energy.Bohr diagram is very interesting and easy to draw. Here, we will draw the Bohr diagram of the Vanadium atom with some simple steps.Steps to draw the Bohr Model of Vanadium atom1. Find the number of protons, electrons, and neutrons in the VanadiumProtons are the positively charged particles and neutrons are the uncharged particles, both these are constituents of the atom nuclei. Electrons are the negatively charged particles that orbit the nucleus of an atomTo find the number of protons an atom contains, just look at its atomic number.If the atomic number of atom is 45, then proton will also be 45, if atomic number is 46, then proton will also be 46.So, the atomic number for Vanadium is 23, hence, the number of protons in the Vanadium atom is also 23.Now, to determine the number of neutrons in an atom, use this formula.⇒ Number of neutrons in atom = Atomic mass of the atom(rounded to the nearest whole number) – Number of proton in an atomFor example, An atom have 33.988 atomic mass and 16 protons.Then, to find the number of neutron, round the atomic mass to the near whole number, so, atomic mass 33.988 round to 34.= (34 – 16 protons) = 18 number of neutrons in the atomNow, To get the number of neutrons in a Vanadium atom, look at its atomic mass which is 50.94 rounded to 51, and the number of protons in Vanadium is 23.∴ Hence, the number of neutrons in Vanadium atom = (51 – 23) = 28It should be noted that “The number of electrons in a neutral atom is equal to the number of protons”.So, the Vanadium atom is neutral, hence, its number of electrons will be equal to the number of protons which is 23 as we already discussed.⇒ The number of electrons in a Vanadium atom = 23⇒ The number of protons in a Vanadium atom = 23⇒ The number of neutrons in a Vanadium atom = 28Let’s read in detail – How to find number of protons, electrons, neutrons?2. Draw the nucleus of an atomA nucleus is a dense and small region that contains the number of protons and neutrons of an atom.In this step, we have to draw a small circle that consists of a number of protons and the number of neutrons of a Vanadium atom.3. Draw the First electron shell“An electron shell may be thought of as an orbit followed by electrons around an atom’s nucleus.”The first electron shell is also called the K-shell, this is the closest shell to the nucleus of an atom and can hold a maximum of two electrons.As we know, the Vanadium atom

ReactionAtom MappingAuto-mappingReaction MechanismsReactionIn Marvin JS there is an option to draw a reaction with the reaction tools.Reaction arrow symbolReaction arrow typeStraight arrowTwo-headed arrow (Resonance arrow.)Equilibrium arrowWith the Reaction tools, you can draw + signs, arrows, and you also can map the reactions.Multi-step reactions and graphical charts also can be created with Reaction tools.Reaction Export - Technical DetailsIf the structure on the canvas contains only a single step reaction, then it will be automatically exported as a reaction file by Marvin JS.This means that, in the exported file, there are separate blocks for reactants, products, and agents, making it possible to use the exported file in a reaction search.In this case, only file formats that support reactions are available in the Export dialog (MRV, RXN, SMILES, CXSMILES, SMARTS, CXSMARTS, CML, RXN V3000, SDF, CSSDF, CDX, SKC).When the structure contains more than one reaction or a multistep reaction (or when the reaction converter web service is not available), the structure will not be converted into a reaction file.In this case, there will not be reactant/product/agent blocks in the exported files, and the + signs and arrows of the reaction(s) will be exported as text characters.{info}Before Marvin JS 16.9.12, the conversion of the structure to a reaction file happened on the server-side and required the reaction converter Web Service. You can try out this with the EXTERNAL property.Atom MappingMarvin JS provides the option to set map numbers to individual atoms. Unlike atom indices, map numbers remain constant during editing the molecule. Mapping can be useful if you want to identify corresponding atoms in the reactant and product side of a reaction.The Atom map visibility must be turned on to display the atom map numbers.There are two ways for adding map numbers to the atoms. You can add map number to every single atom manually from the Atom properties dialog or if you would like to map the same atom with the same number, you can map these atoms by dragging from atom to atom when the Reaction tool is active. Both ways are suitable for changing or deleting the corresponding numbers.Auto-mappingClick the Auto map button. In this case, every atom in the reaction would get an atom map number automatically.{primary}The auto-map function only works for structures that are in the same reaction, that is, there must be only one reaction (one arrow) on the canvas where every molecule would be a reactant or a product of it.Reaction MechanismsMarvin JS supports the detailed display of reaction mechanisms by using electron flow arrows (or mechanism arrows) to describe the formation and breaking of chemical bonds.Electron flow arrows describe the movement of electrons in the elementary reaction steps of a complex mechanism.In Marvin JS, you can choose between two types of electron flow arrows:Electron flow arrow symbolElectron flow arrow typeElectron flow single arrowElectron flow double arrowIf you want an atom to be the source of an electron flow arrow, the atom has to have a radical electron or a lone pair. Lone pair visibility must be

Color component, range is 0.0 to 1.0highlight – uses highlight color and line width or not, icon and textwill drawn in highlight colortext – draw text if it’s not NULL, if it’s drawn then icon is hiddenicon – one of the GRAPHICS_ICON values listed at the top of the fileReturns:handle of the marker, on error this function returns -1.schrodinger.maestro.maestro.create_atom_quad_marker(atom1, atom2, atom3, atom4, r, g, b, hr, hg, hb, highlight, text, icon=0)¶Create a 2D atom quad marker.Parameters:atom1 – is the first atom numberatom2 – is the second atom numberatom3 – is the third atom numberatom4 – is the fourth atom numberr – is the red color component, range is 0.0 to 1.0g – is the green color component, range is 0.0 to 1.0b – is the blue color component, range is 0.0 to 1.0hr – is the highlight red color component, range is 0.0 to 1.0hg – is the highlight green color component, range is 0.0 to 1.0hb – is the highlight blue color component, range is 0.0 to 1.0highlight – uses highlight color and line width or not, icon and textwill drawn in highlight colortext – draw text if it’s not NULL, if it’s drawn then icon is hiddenicon – ne of the GRAPHICS_ICON values listed at the top of the fileReturns:handle of the marker, on error this function returns -1.schrodinger.maestro.maestro.get_temp_location()¶Returns a path to a temporary directory which is likely to bewriteable and will be removed when this Maestro session isfinished. This would typically used when temporary files needto be created, for example if file conversion is required aspart of a script workflowRebuild the scripts menu (includes entries for both Knime Workflows andcustom python scripts menus). This will re-read the scriptsx.mnu file fromthe user and common areas and display the contents in the Scripts menu.schrodinger.maestro.maestro.write_entries_from_project(filename, which_entries, Htreatment=None, synchronize=True, append=False, props=True)¶Write

How to Draw Lewis Dot Structure : A step-by-step GuideLewis dot structure is the classical bonding model in which only valence electrons of the atoms are used. Lewis structure is very important in chemistry, because they are used in many important concepts of general chemistry such as chemical bonding, resonance, valence shell electron pair repulsion theory, prediction of the polarity of the molecules and understanding of reaction mechanisms. Hence it is very important to learn how to draw Lewis Dot structure correctly for an atom, ion, molecule, polyatomic ion and an ionic compound.We can learn to make accurate Lewis dot structures in 4 simple steps. These steps are easy to understand and implement. Do not skip or try to rearrange any step during your learning process, as it is important to understand and implement each step to correctly design these structures. Once you master these, you can draw Lewis structure of any chemical entity quickly. In these steps, you will come across some terms like valence electrons ,electronegativity, stable electronic configuration, formal charges, bonding pair and lone pair, single ,double and triple bonds .If you do not know the meaning of any of these terms, do not worry as all terms will be explained in the explanation of each step .STEP 1 : COUNT THE TOTAL VALENCE ELECTRONS.In Lewis dot structure, only valence electrons are used for making of the structure. Valence electrons are the electrons present in the outermost shell of the electronic configuration of an atom. The example

Component, range is 0.0 to 1.0b – blue color component, range is 0.0 to 1.0hr – highlight red color component, range is 0.0 to 1.0hg – highlight green color component, range is 0.0 to 1.0hb – highlight blue color component, range is 0.0 to 1.0highlight – uses highlight color and line width or not, icon willdrawn in highlight coloricon – is one of the GRAPHICS_ICON_* values listed at the top of thefile.style – is a style for atom markers eitherGRAPHICS_ATOM_MARKER_STYLE_STAR orGRAPHICS_ATOM_MARKER_STYLE_GENERALReturns:handle of the marker, on error this function returns -1schrodinger.maestro.maestro.create_atom_pair_marker(atom1, atom2, r, g, b, hr, hg, hb, highlight, text, icon=0)¶Create a 2D atom pair marker.Parameters:atom1 – first atom numberatom2 – second atom numberr – red color component, range is 0.0 to 1.0g – green color component, range is 0.0 to 1.0b – blue color component, range is 0.0 to 1.0hr – highlight red color component, range is 0.0 to 1.0hg – highlight green color component, range is 0.0 to 1.0hb – highlight blue color component, range is 0.0 to 1.0highlight – uses highlight color and line width or not, icon and textwill drawn in highlight colortext – draw text if it’s not NULL, if it’s drawn then icon is hiddenicon – one of the GRAPHICS_ICON values listed at the top of the fileReturns:handle of the marker, on error this function returns -1schrodinger.maestro.maestro.create_atom_triple_marker(atom1, atom2, atom3, r, g, b, hr, hg, hb, highlight, text, icon=0)¶Create a 2D atom triple marker.Parameters:atom1 – first atom numberatom2 – second atom numberatom3 – third atom numberr – red color component, range is 0.0 to 1.0g – green color component, range is 0.0 to 1.0b – blue color component, range is 0.0 to 1.0hr – highlight red color component, range is 0.0 to 1.0hg – highlight green color component, range is 0.0 to 1.0hb – highlight blue