ODYSSEY
Bug Fixes / Known Issues
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Experiments
Experiment 1, States of Matter, Worksheet
The temperature and/or pressure of six of the ten samples of chlorine is not the one stated.
Experiment 1, States of Matter, Worksheet (Student Edition only)
The answers to Questions 1 and 4 are partially displayed.
Experiment 2, Elements, Compounds, and Mixtures, Page C
For the second compound it should say at the end of its description:
Among the properties of
nickel tetracarbonyl is its high toxicity.
Experiment 2, Elements, Compounds, and Mixtures, Page F
The oily component is
neopentane (not
n-pentane).
Experiment 3, Physical Properties, Page A
Last paragraph: The temperature value of the system is not automatically displayed when the "Properties" panel is
brought up (the user must select "Thermodynamics
Temperature").
Experiment 3, Intensive and Extensive Properties, Page A
Last paragraph: The temperature value of the system is not automatically displayed when the "Properties" panel is
brought up (the user must select "Thermodynamics
Temperature").
Experiment 3, Physical Properties, Worksheet
The SO
2 molecules of the three gas samples all have single bonds
(instead of double bonds) and carry an erroneous net charge of +2
Experiment 3, Physical Properties, Worksheet
The "PDF File" option at the bottom of the page links to an outdated version of the document
Experiment 3, Physical Properties, Worksheet
1)"Composition
Number of Molecules" should be "System
Total Number of Molecules."
2) The properties "Thermodynamics
Pressure" and
"Other
PV/nRT"
are not available (however, in the Instructor's Edition they can be made available by switching to
Expert Mode).
Experiment 3, Physical Properties, Worksheet (Instructor's Edition only)
In the WORD-formatted worksheets,
"Thermodynamics
PV/nRT" should be
"Other
PV/nRT".
Experiment 3, Intensive and Extensive Properties, Worksheet
"Composition
Number of Molecules" should be "System
Total Number of Molecules."
Experiment 3, Physical Properties, Worksheet (Japanese version only)
"Thermodynamics
PV/nRT" should be "Other
PV/nRT"
Experiment 3, Physical Properties, Worksheet (Student Edition only)
The answers to some of the questions are revealed.
Experiment 3, Intensive and Extensive Properties, Worksheet (Student Edition only)
The answers to some of the questions are revealed.
Experiment 3, Physical Properties, Worksheet Answers (Instructor's Edition only)
"Pressure" missing from the listed answer to Question 3
Experiment 4, Chemical Energy, Page C (Student Edition only)
Bungled text in the second half of the page (part of an erroneously placed Instructor's Comment)
Experiment 4, Chemical Energy, Page D
"2,000,000 kJ/mol per mol" should be "2,000,000 kJ/mol".
Experiment 4, Chemical Energy, Page D
Energy of reaction of nitroglycerin given for 4 moles of reactant, not 1 mol
Experiment 4, Heat Capacity, Page A (Windows Instructor's Edition only)
Under certain circumstances, the "K" and "mol" units of the ideal gas constant
R do not show their "1" exponents (in the first comment of the page).
Experiment 4, Heat Capacity, Worksheet
Very briefly (between ~0.8 and ~1.0 picosec), the heat capacity of the sample of
iron is displayed with an erronously large value.
Experimento 4, La capacidad calorífica, Hoja de trabajo (ODYSSEY Español)
Very briefly (between ~0.8 and ~1.0 picosec), the heat capacity of the sample of
iron is displayed with an erronously large value.
Experiment 7, Conservation of Energy, Pages A and C
Potential and total energy initialized incorrectly (
values jump when executing the first time step)
Experiment 7, Rotations and Vibrations, Page D (Macintosh version only)
The denominator of the ratio at the end of the page will not get filled in
even if the simulation is running. As a consequence, the value of the ratio remains at "NaN.NaN".
Experiment 8, Heat Capacity, Page A (Windows Instructor's Edition only)
Under certain circumstances, the "K" and "mol" units of the ideal gas constant
R do not show their "1" exponents (in the first comment of the page).
Experiment 8, Heat Capacity, Worksheet
Incorrect molar mass displayed for "Copper" and "Iron".
Experiment 8, Reaction Energy, Page D
"2,000,000 kJ/mol per mol" should be "2,000,000 kJ/mol".
Experimento 8, Energía de reacción, Página D (ODYSSEY Español)
"2,000,000 kJ/mol por mol" should be "2,000,000 kJ/mol".
Experiment 10, Atomic Orbitals, Page A (Instructor's Edition only)
Characterization of isosurfaces applies to electron densities, not orbitals.
Experiment 10, Atomic Orbitals, Page A (Student Edition only)
Non-belonging sentence fragment in the middle of the page: "...atomic orbitals) involves a
number of approximations and assumptions."
Experiment 10, Atomic Orbitals, Page B (Student Edition only)
Orphaned, non-belonging sentence: "Any such coordinate system would be arbitrary"
Experiment 10, Atomic Orbitals, Pages C and D
While all radiobuttons work correctly (i.e., clicking on a button displays an orbital as indicated),
a given button does not necessarily get "set" after its action has been executed.
Experiment 11, d-Orbitals
While all radiobuttons work correctly (i.e., clicking on a button displays an orbital as indicated),
a given button does not necessarily get "set" after its action has been executed.
Experiment 12, Ionic Size vs. Atomic Size, Page A
At the bottom of the page it should say: "The sodium atom has a partly populated
n = 3 shell..."
(rather than
n = 4 shell).
Experiment 12, Ionic Radii, Page A
At the bottom of the page it should say: "The sodium atom has a partly populated
n = 3 shell..."
(rather than
n = 4 shell).
Experiment 12, Ionic Radii, Worksheet (Student Edition only)
The answer to the third question is revealed.
Experiment 12, Ionic Radii, Worksheet (Japanese version only)
Towards the bottom of the page the "low electron density" hyperlink for the nitrogen atom is inoperative.
Experiment 13, Isoelectronic Ions, Page A
Principal quantum number of sodium valence erroneously given as
n = 4 instead of
n = 3
Experiment 13, Isoelectronic Ions, Page A
The density surfaces of the first model (O
2) will not display
if the page is reached by scrolling forward from the
Worksheet of the previous (Ionic Size vs. Atomic Size)
experiment.
Remedy: Reload the page.
Experiment 13, Isoelectronic Ions, Page A
The density surfaces of the first model (O
2) will not display
if the page is reached by scrolling forward from the
Worksheet of the previous (Ionic Radii)
experiment.
Remedy: Reload the page.
Experiment 13, Isoelectronic Ions, Page A (Windows version only)
The density surfaces of the first model (O
2) will not display
if the page is reached by scrolling forward from the
Worksheet of the previous (Ionic Radii)
experiment.
Remedy: Reload the page.
Experimento 13, Iones isoelectrónicos, Página A (ODYSSEY Español)
The density surfaces of the first model (O
2) will not display
if the page is reached by scrolling forward from the
Worksheet of the previous (Ionic Radii)
experiment.
Remedy: Reload the page.
Experiment 14, Ionic Bonding (Japanese version only)
The topic cannot be opened from the
English-language table of contents (opening
from the Japanese-language table of contents works correctly).
Experiment 14, Ionic Bonding, Page C
Stoichiometric coefficient of "1/2" (for Cl
2) missing in the second reaction equation
Experiment 14, Energetics of Ionic Bond Formation, Page A (Macintosh version only)
The energy for the two ions at a distance of "
r = 237 pm" does not display.
As a consequence, the summed energy terms (for "coming together of the two ions,"
for "electrostatics," and for "bond energy") also don't display correctly.
Experimento 14, La energía de enlaces iónicos, Hoja de trabajo (ODYSSEY Español para profesores)
If used with a European version of Windows, not all of the numerical data in the Answer Key will display with the appropriate European number formatting.
Experiment 15, Covalent Bonding, Page A and Worksheet
The "step-by-step arrows" surrounding the distance slider at the top of the textpanel are inoperative
(the slider itself works correctly)
Experiment 15, Covalent Bonding, Page D (Windows Instructor's Edition only)
Under certain circumstances, the following "two energetic effects" in the first comment are not shown:
1) A
favorable energy term because of the now increased electrostatic attraction between core electrons and nuclei (shorter distance).
2) An
unfavorable quantum mechanical energy term because the core electronic density is now confined to an even smaller space than before.
Experiment 15, Covalent Bonding, Page D (Windows Instructor's Edition only)
Under certain circumstances, the subscript and superscript of the H
2+ formula at the end of the second comment are not shown.
Experiment 16, Covalent Bonding, Page D (Windows Instructor's Edition only)
Under certain circumstances, the subscript and superscript of the H
2+ formula at the end of the second comment are not shown.
Experiment 16, Bond Polarity, Worksheet (Instructor's Edition only)
The WORD-formatted worksheet includes a question (#6) that does not belong there.
Experiment 17, Bond Polarity, Worksheet (Instructor's Edition only)
The WORD-formatted worksheet includes a question (#6) that does not belong there.
Experiment 20, Electron Pair Geometry, Page C
HCN shown with a quadruple bond instead of triple bond
Experiment 20, Electron Pair Geometry, Page D
ClF
2+ mislabeled (as ClO
2+)
Experiment 20, Electron Pair Geometry, Page E
The SOF
4 molecule should show the oxygen atom in an equatorial position
rather than an axial position.
Experiment 20, VSEPR Theory, Page E
The SOF
4 molecule should show the oxygen atom in an equatorial position
rather than an axial position.
Experimento 20, Repulsión de pares de electrones de valencia, Página E (ODYSSEY Español)
The SOF
4 molecule should show the oxygen atom in an equatorial position
rather than an axial position.
Experiment 20, Electron Pair Geometry, Page E
On certain computers, the lone pairs of the XeF
2 molecule will be misplaced
on reorienting the molecule.
Experiment 20, VSEPR Theory, Page E
On certain computers, the lone pairs of the XeF
2 molecule will be misplaced
on reorienting the molecule.
Experiment 21, Molecular Geometry
On certain computers, the lone pairs of the XeF
2 molecule will be misplaced
on reorienting the molecule.
Experiment 21, Molecular Shapes
On certain computers, the lone pairs of the XeF
2 molecule will be misplaced
on reorienting the molecule.
Experiment 22, Dipole Moments, Page A
Definition of unit of "Debye" with incorrect exponent
Experiment 22, Dipole Moments, Page A (Windows Instructor's Edition only)
Under certain circumstances, the value of the electrostatic unit is shown without its exponent:
1 electrostatic unit = 3.34·10
10 C.
Experiment 23, Density of Gases, Page B (Macintosh version only)
In the next-to-last paragraph, the number of molecules is not displayed.
The value is "100".
Experiment 23, Density of Gases, Worksheet
"Composition
Number of Molecules" should be "System
Total Number of Molecules."
Experiment 23, Density of Gases, Worksheet (Student Edition only)
The answer to the last question is revealed.
Experiment 24, Motion of the Molecules in a Gas, Worksheet
Using the "Collisions" link within the text turns on the visualization of
all collisions
(molecule-molecule as well as molecule-wall) rather than only the visualization of
molecule-molecule collisions. However, the subsequent "Collision Density (Molecule-Molecule)"
measurement in fact only counts molecule-molecule collisions.
Remedy: Use
"Model
Customize..." to adjust the setting for collision visualization.
Experimento 24, El movimiento de las moléculas en gases, Hoja de trabajo (ODYSSEY Español)
Using the "Collisions" link within the text turns on the visualization of
all collisions
(molecule-molecule as well as molecule-wall) rather than only the visualization of
molecule-molecule collisions. However, the subsequent "Collision Density (Molecule-Molecule)"
measurement in fact only counts molecule-molecule collisions.
Remedy: Use
"Model
Customize..." to adjust the setting for collision visualization.
Experiment 24, Motion of the Molecules in a Gas, Annotation Page
Experiment cannot be annotated
Experiment 25, Forces between Gas Molecules, Page A
Turning on the "Trail" display turns on the trails of
all atoms
(not just one as the text suggests)
Experiment 25, Forces between Gas Molecules, Page B
Following scripted links won't change the model style of the selected particle to Space Filling
Experiment 25, Forces between Gas Molecules, Worksheet
Problem #4: Instructions erroneously call for entering a new ethyne pressure of "15,000"
(with a comma separator) if the pressure unit is set to kPa.
(In fact, the new pressure has to be entered as "15000",
without a comma separator.)
Experiment 29, Ability of Gases to Mix, Page A
The CO molecules are single-bonded rather than triple-bonded.
Experiment 29, Ability of Gases to Mix, Worksheet
Program sometimes crashes on changing the composition of the second or third system
Experiment 29, Ability of Gases to Mix, Worksheet
The "PDF File" option at the bottom of the page links to an outdated version of the document
Experiment 29, Ability of Gases to Mix, Worksheet
Velocities of the two components get initialized in the physically wrong order (Krypton speeds higher than fluorine speeds; opposite would be correct)
Experiment 33, Universality of the Ideal Gas Law, Page B
The volume of 1 mol of ideal gas at 25°C is 24.5 L, not 22.4 L (which is the volume at 0°C)
Experiment 34, Mole Fractions, Page A
The
mass data in the first paragraph update correctly only for the first two of the
three available gas mixtures (pull-down menu in the upper left corner),
i.e., there is no updating for SF
6/N
2/He.
Experiment 35, Molecular Speeds in a Gas, Worksheet
UF
6 being simulated at higher temperature than indicated in Properties panel (~500-600 K instead of 300 K)
Experiment 35, Molecular Speeds in a Gas, Worksheet (Student Edition only)
The answer to the fourth question is revealed.
Experiment 36, Maxwell-Boltzmann Distribution, Page C
Incorrect implication concerning the asymmetry of the kinetic energy distribution.
Experiment 36, Maxwell-Boltzmann Distribution, Page C (Student Edition only)
Non-belonging sentence fragment towards the middle of the page:
barometric formula).
Experiment 36, Maxwell-Boltzmann Distribution, Worksheet (Instructor's Edition only)
The WORD-formatted worksheet misrepresents in Question #5 the operation of the Refresh/Reload function.
Experiment 37, Speed Distribution and Temperature, Page A
The nitrogen molecules are single-bonded rather than triple-bonded.
Experiment 37, Speed Distribution and Temperature, Worksheet (Instructor's Edition only)
The WORD-formatted worksheet lacks the complete set of instructions for generating the plot.
Experiment 38, Speed Distribution and Molar Mass, Worksheet (Instructor's Edition only)
The WORD-formatted worksheet lacks the complete set of instructions for generating the plot.
Experiment 39, Speed Distribution for Gas Mixtures, Page A
Some of the CO molecules are single-bonded rather than triple-bonded.
Experiment 39, Speed Distribution for Gas Mixtures, Page B
The calculated kinetic energy distribution is artificially shifted towards somewhat high energies
Experiment 40, Effusion, Worksheet
Some of the CO molecules are single-bonded rather than triple-bonded.
Experiment 40, Effusion, Worksheet (Student Edition only)
Orphaned, non-belonging sentence fragment at the end of the page.
Experiment 42, Gases at High Pressure, Page A
The given definition of the compression factor does not make clear that
V is the
molar volume.
Experimento 42, Gases a alta presión, Página A (ODYSSEY Español)
Because of a bug in Microsoft Internet Explorer, the pressure for sample I is shown as "0 atm" instead of "1 atm".
Experiment 42, Gases at High Pressure, Pages A and B
The model of ammonia used for sample I is different from the model used for samples II, III, and IV.
Experiment 42, Gases at High Pressure, Page B
The compression factor for sample III should in fact be ~1.0 as claimed and the compression
factor for sample IV should be higher than shown, namely ~1.6.
Experimento 42, Gases a alta presión, Página B (ODYSSEY Español)
The compression factor for sample III should in fact be ~1.0 as claimed and the compression
factor for sample IV should be higher than shown, namely ~1.6.
Experiment 43, Molecular Characteristics of Liquids, Page A/B
Following scripted links will only turn on
one trail (rather than all trails).
Experiment 43, Molecular Characteristics of Liquids, Worksheet
Omits to state at top of page that
bromine is a liquid under ambient conditions
Experiment 44, Molecular Characteristics of Solids, Worksheet (Instructor's Edition only)
In the answer to Question 2 it should say: While molecular
motion affects the degree of symmetry...
Experiment 45, Molecular Motion, Page A and Worksheet
The "state" of the display of molecular trails (either "On" or "Off") may change when switching samples
Experimento 45, Movimiento molecular en líquidos y sólidos, Hoja de trabajo (ODYSSEY Español)
For the gas phase of water, the direction of the molecular dipoles is exactly the opposite
of what it should be (the models for the liquid and solid phases are correct).
Experiment 46, Energies of Gases, Liquids, and Solids, Worksheet (Instructor's Edition only)
The WORD-formatted worksheet should refer to "Argon" and "Xenon" (instead of "Argon" and "Water").
Experiment 47, Intermolecular Forces, Page A (Windows Instructor's Edition only)
In the comment at the bottom of the page, the exponent is missing from the "mass of individual atoms and molecules"; the correct value is ~10
26 kg.
Experiment 47, Intermolecular Forces, Page B
Methane, n-heptane, and n-octadecane have 10, 58, and 146 electrons, respectively
(rather than the numbers claimed)
Experiment 47, Intermolecular Forces, Page B
The molecular model of octadecane does not only show "one molecule" as asserted
Experiment 48, Ion-Dipole Forces, Page B
Must click on underlined words (
not radiobuttons) to make charges turn on/off
Experiment 48, Ion-Dipole Forces, Page C
Must click on underlined words (
not radiobuttons) to make charges turn on/off
Experiment 49, Hydrogen Bonding, Page B
HCl sample should be at T = 10°C (instead of T = 25°C)
Experiment 49, Hydrogen Bonding, Worksheet Answers (Instructor's Edition only)
Stated answers for systems I and IV neglect hydrogen bonding interactions
where the non-water component acts as the acceptor for two water molecules
Experiment 49, Hydrogen Bonding, Pages A, B, C, and Worksheet
The "state" of the display of hydrogen bonds (either "On" or "Off") may change when switching samples
Experiment 51, Ice
The ice lattice develops defects during extended simulations.
Experiment 51, Ice (Macintosh version only)
The ice lattice develops defects during extended simulations.
Experiment 52, Melting Transition
Even prior to melting, the ice lattice develops defects during extended simulations.
Experiment 52, Melting Transition (Macintosh version only)
Even prior to melting, the ice lattice develops defects during extended simulations.
Experiment 54, Cubic Crystal Lattices, Page A
Some atoms incorrectly colored
Experiment 54, Cubic Crystal Lattices, Page D
The extra lattice points are shown not in red, but
blue.
Experiment 53, Cubic Crystal Lattices, Page D
The extra lattice points are shown not in red, but
blue.
Experimento 53, Celdas cúbicas cristalinas, Página D (ODYSSEY Español)
The extra lattice points are shown not in red, but
blue.
Experiment 55, Close Packing in Metals, Page B
Incorrect atom coloring for models 24 and 25
Experiment 57, Molarity and Molality, Worksheet
From the viewpoint of organic chemistry, "benzoyl peroxide in acetonitrile" is
a poor example of a solution (the solute would probably oxidize the solvent)
Experiment 57, Molarity and Molality, Worksheet
Converting from molarity to molality using the density of the solution involves a poor approximation
(the correct molality is 0.30 mol/kg, not 0.28 mol/kg)
Experiment 59, Structure of Solutions, Worksheet
The "display state" for the solvation shell (either "Show Shell Only" or "Show All") may change when switching samples
Experiment 59, Energy of Solutions, Page A
The lattice energy shown is not correct (to display the correct energy: click on the background,
click "SHIFT-O" (capital letter "O"), replace the keyword "ATOM_BASE" by "GROUP_BASE", and click OK.)
Experiment 60, Energy of Solutions, Page B
Measured hydration energies come out larger than claimed in the text (because of favorable interactions with counterions)
Experiment 61, Hydration Energy and Ionic Size, Worksheet (Instructor's Edition only)
The WORD-formatted worksheet erroneously associates the "Binding Energy, Molecule" property with the "Electrostatics" menu (instead of the "Energy" menu).
Experiment 60, Hydration Energy and Ionic Size, Worksheet (Instructor's Edition only)
The WORD-formatted worksheet erroneously associates the "Binding Energy, Molecule" property with the "Electrostatics" menu (instead of the "Energy" menu).
Experiment 60, Hydration Energy and Ionic Size, Worksheet
As an unintended consequence of the recent internationalization of
ODYSSEY,
the plot at the center of the worksheet can no longer be generated.
Remedy: Use
any version of
ODYSSEY prior to release 2.4.
Experimento 60, Energía de hidratación y tamaño iónico, Hoja de trabajo (ODYSSEY Español)
As an unintended consequence of the recent internationalization of
ODYSSEY,
the plot at the center of the worksheet can no longer be generated.
Remedy: Use
any version of
ODYSSEY prior to release 2.4.
Experiment 62, Hydration Energy and Ionic Charge, Worksheet
Zinc ion is mislabeled as "Zinc"
Experiment 68, Hydration Energy and Ionic Charge, Worksheet
Curve fit of "Linear" does not generate two separate curves for cations and anions
as would be physically required
Experiment 61, Hydration Energy and Ionic Charge, Worksheet
As an unintended consequence of the recent internationalization of
ODYSSEY,
the plot at the center of the worksheet can no longer be generated as instructed
(only the datapoints for the anions will display).
Remedy: Use
any version of
ODYSSEY prior to release 2.4.
Experimento 61, Energía de hidratación y carga iónica, Hoja de trabajo (ODYSSEY Español)
As an unintended consequence of the recent internationalization of
ODYSSEY,
the plot at the center of the worksheet can no longer be generated as instructed
(only the datapoints for the anions will display).
Remedy: Use
any version of
ODYSSEY prior to release 2.4.
Experiment 65, Organic Acids
Experimental acid ionization constant of ethanoic (acetic) acid should be given as 1.8·10
5
Experiment 64, Procesos espontáneos, Página A (ODYSSEY Español)
Query of the entropy
prior to removal of the confining barrier leads to an incorrect value.
Experiment 66, Spontaneous Processes, Page A
The nitrogen molecules change from being triple-bonded to erroneously being single-bonded as soon as the simulation starts.
Experiment 64, Spontaneous Processes, Page A
The nitrogen molecules change from being triple-bonded to being erroneously single-bonded as soon as the simulation starts.
Experiment 68, Entropy and Temperature, Page B
Incorrect generalization of effort for entropy calculation
Experiment 69, Chelates, Page A
[Cu(en)(NCS)
2] mislabeled
Experiment 70, Structural Isomers, Page A
[Co(NH
35)(SCN)]
2+ and [Co(NH
35)(NCS)]
2+ incorrectly labeled with net charges of +1
Experiment 68, Structural Isomers, Page B
The hyperlinked solution sample at the bottom of the page comes up with a non-fatal script error.
Also, the "simulation" hyperlink that directly follows is non-functional because of a persistent script error;
simple remedy: use the
Start/Stop button below the model.
Experiment 71, Stereoisomers, Page B
[Cr(C
2O
4)
3]
3- is mislabeled in the drop-down menu.
Experiment 71, Stereoisomers, Page B
[Zn(en)
2]
2+ is
not chiral
Experiment 71, Stereoisomers, Page B
The next to last paragraph should start: "As previously for the octahedral
chromium complex, it is impossible..."
Experiment 71, Stereoisomers, Worksheet Answers (Instructor's Edition only)
[Pt(NH
3)BrClF]
- is
not chiral
Experiment 74, Alcohols, Worksheet
The "state" of the display of hydrogen bonds (either "On" or "Off") may change when switching samples
Experiment 74, Alkynes, Worksheet
In Question 5, the labels ("Low" / "High") for the electron density buttons need to be swapped.
Experimento 74, Alquinos, Hoja de trabajo (ODYSSEY Español)
In Question 5, the labels ("Low" / "High") for the electron density buttons need to be swapped.
Experiment 78, Carboxylic Acids, Worksheet (Macintosh version only)
On slow machines, the embedded hyperlinks may be nonfunctional.
Remedy: Reload the page.
Experiment 75, Carbohydrates, Page D
In the model of amylose, 3 of the 10 glucose rings are missing a hydrogen in C-1 position.
Molecular Stockroom
Agua (ODYSSEY Español)
For the gas phase sample, the direction of the molecular dipoles is exactly the opposite
of what it should be (the other models are correct).
Alcohols
Bad HTML link for Cyclohexanol/Molecule (but sample is still accessible from the drop-down menu)
Alkanes, Linear
Hexadecane/Molecule mislabed in drop-down menu as "Heptadecane"
Alkylbenzenes
The sample of liquid xylene includes two cases of unphysically "interlocked" molecules
Amines
Doesn't indicate that methyl amine is a liquid only at reduced temperature
Amino Acids
Solutions of glutamic acid and lysine simulated
with incomplete force description (intrasolute interactions beyond 1-4 terms missing)
Amino Acids in Water
Solutions of glutamic acid and lysine simulated
with incomplete force description (intrasolute interactions beyond 1-4 terms missing)
Amylose
In the biopolymer chain, 3 of the 10 glucose rings are missing a hydrogen in C-1 position.
The corresponding hydrogen is also missing in the model of the monomer (glucose).
Carbon
Graphite model slightly inaccurate
Carboxylic Acids
The two models for the molecule and solid of
Oxalic Acid (Ethanedioic Acid) cannot be invoked via the radiobuttons
in the "Polycarboxylic" section at the bottom of the page.
Remedy: Use the pull-down
menu in the upper left corner instead (the two last items are for Oxalic Acid).
Chromium Complexes
[Cr(C
2O
4)
3]
3- mislabeled in page
Chromium Complexes
[Cr(C
2O
4)
3]
3- is mislabeled in the drop-down menu.
Cholesterol in Chloroform
Flawed simulation (intrasolute interactions beyond 1-4 terms missing)
Cobratoxin
Simulation functionality should be disabled
Complejos de cobre (ODYSSEY Español)
The molecular charge of [Cu(NH
3)
4(H
2O)
2]
2+ is displayed incorrectly when queried in the "Properties" table.
Complejos de platino (ODYSSEY Español)
The molecular charge of most of the complexes on the page is displayed incorrectly when queried in the "Properties" table.
Copper Complexes
The molecular charge of three of the four complexes on the page is displayed incorrectly when queried in the "Properties" table.
Copper Complexes
The molecular charge of [Cu(NH
3)
4(H
2O)
2]
2+ is displayed incorrectly when queried in the "Properties" table.
Crambin
a-helical
α-helical
EDTA
The anion's charge map (electrostatic potential map) is missing.
Esters
The correct systematic name of vinyl acetate is "ethenyl ethanoate" (not "propenyl ethanoate").
Esters
Drop-down menu in the upper left corner shows incorrect systematic name for vinyl acetate
(but the name shown in the text sectionethenyl ethanoateis correct)
Ethanol-Water
Invalid link in the "Individual Items" listing.
Remedy: Directly open model of "Wine" instead.
Folic Acid in Ethanol
Flawed simulation (intrasolute interactions beyond 1-4 terms missing)
Fullerene
Invalid link in the "Individual Items" listing.
Remedy: Open "Carbon" instead.
Halide Ions in Water
Iodide ion should not be chargeless
Helium
Normal boiling point is -269°C (not -259 °C)
Hemoglobin
Model contains extraneous hydration water molecules
Interhalogens
Simulation functionality for BrF
5 should be disabled
Interhalogens
a) Molecular charge is incorrect for the cation and the two anions.
b) Atomic charges of the uncharged molecules sometimes correspond to unphysical bond polarities.
Interhalogens
Saving IF
7 in the
.odydata file format will make the program crash.
Compuestos interhalogenados (ODYSSEY Español)
Saving IF
7 in the
.odydata file format will make the program crash.
Iron
Simulation functionality of high temperature γ-phase should be disabled
KMnO4 in Water (Instructor's Edition only)
Incorrectly implied that color is due to d-d transitions
Lead Chlorides
Name string for lead dichloride is misformatted
Methylpropanol
Misspelled in the "Individual Items" listing.
Mixtures with Acetone
Invalid link in the "Individual Items" listing.
Remedy: Use the listing by category (open "With Acetone..." in the "Mixtures" section).
Nanotubes
Invalid link in the "Individual Items" listing.
Remedy: Open "Carbon" instead.
Nitrogen
The molecules of the
liquid phase are single-bonded rather than triple-bonded
(the other models are not affected).
Nitrógeno (ODYSSEY Español)
The molecules of the
liquid phase are single-bonded rather than triple-bonded
(the other models are not affected).
Nitrogen Oxides
The molecules of the NO
2 (g) sample indicate an erroneous large dipole moment
(the true dipole moment is zero as there are no net atomic charges)
1-Octanol-Water
Bad model (octanol component simulated incorrectly)
Orbitales de hidrógeno, H2 (ODYSSEY Español)
The correct label for the molecular orbital is "1s σ".
Orbitales de oxígeno, O2 (ODYSSEY Español)
The orbital labels for the two anti-bonding orbitals should include "stars".
Oxygen
Solid sample (removed from Release 1.3 on):
Unit cell should be shown as monoclinic, not orthorhombic; required temperature is < -247°C
Pain Medications
Fourth compound should be "Naproxen" (the correct model can be found
in Experiment 76
Worksheet
Question 3).
Palladium Complexes
[Pd(NH
3)
3(NO
2)]
+ is mislabeled in the drop-down menu.
Complejos de paladio (ODYSSEY Español)
[Pd(NH
3)
3(NO
2)]
+ is mislabeled in the drop-down menu.
Phospholipase Inhibitor
Simulation functionality should be disabled
Platinum Complexes
The order of the complexes is scrambled.
Remedy: Use the drop-down menu in the upper left corner to navigate among complexes.
Platinum Complexes
The molecular charge of most of the complexes on the page is displayed incorrectly when queried in the "Properties" table.
Platinum Complexes
The charge of two last complexes is given incorrectly in the drop-down menu in the upper left corner
(but next to the radiobuttons on the right it is given correctly).
Complejos de platino (ODYSSEY Español)
The charge of two last complexes is given incorrectly in the drop-down menu in the upper left corner
(but next to the radiobuttons on the right, it is given correctly).
Polieteno (Polietileno) (ODYSSEY Español)
The correct recycling code for
High Density Polyethylene is "2" (instead of "1").
Polyethylene
The correct recycling code for
High Density Polyethylene is "2" (instead of "1").
Polyethene (Polyethylene)
The correct recycling code for
High Density Polyethylene is "2" (instead of "1").
α-Quartz
Unit cell should be shown orthorhombic ( = supercell of trigonal primitive cell), not cubic
Ricin
Model contains extraneous organic material (solvent, etc.)
Sales de plata (ODYSSEY Español)
The silver ions are erroneously uncharged.
Seawater
Concentration of magnesium in real seawater is
about
half as much as in the model shown (not twice as much)
Silver Salts
The silver ions are erroneously uncharged.
Soap Solution
Bad simulation because of missing intramolecular Van der Waals terms
Sulfur Oxides
Molecules of the SO
2 (g) sample have single bonds (instead of double bonds) and carry a net charge of +2
Superoxide Dismutase
Model contains extraneous hydration water molecules
Syngas
Initial speeds after starting dynamics incorrect
Syngas
Some of the carbon monoxide molecules are single-bonded rather than triple-bonded.
Gas de síntesis (ODYSSEY Español)
Some of the carbon monoxide molecules are single-bonded rather than triple-bonded.
Thioredoxin
Simulation functionality should be disabled
Transition Metal Ions in Water
The models for Cr
3+ and Cu
2+ need to be swapped
Triethyl Phosphine Oxide
Model (listed when using "List Individual Entries") is missing
(Model removed in later releases)
Triose Phosphate Isomerase
Model contains extraneous hydration water molecules
UF6-Hydrogen
Molecular speeds not in the correct ratio for the two components
Uranium Hexafluoride
Temperature is higher than indicated in the Properties panel (~500-600 K instead of 300 K)
Vasopressin in Water
System locks up after ~1.09 picosec simulation time
Water
The structure of solid water (ice) develops defects during extended simulations.
Water (Macintosh version only)
The structure of solid water (ice) develops defects during extended simulations.
Zinc Blende
Chemical formula is ZnS, not ZnS
2
Zinc Complexes
[Zn(en)
2]
2+ is
not chiral
Model Kit
Shortcut Key for New Build Panel (Windows version only)
The "Ctrl+N" shortcut key (for "File
New") doesn't work.
Switching Among Build Panels (under Windows 2000 only)
If the model kit is opened with File
New, the build panel remains in the "Entry-Level" setting, i.e., the so-called combobox for
switching among panels is inoperative.
Remedy: You can still switch among build panels using the "Up" and "Down" keys
on the keyboard.
Adding New Components to Stockroom Models
Adding a new component to certain stockroom models can sometimes make the program
crash (an example is the addition of a noble gas to stockroom models of gaseous nitrogen or gaseous hydrogen).
Remedy: Build the entire model from scratch rather than on the basis of an existing
stockroom model.
Large DPI Settings on High Resolution Screens (Windows version only)
The "Build" and "Cell" panels may be somewhat misformatted if a high resolution screen is used in
conjunction with a large DPI setting.
Orientation of Inserted Fragments
The bond of monovalent atoms is turned away from the viewer when first inserting such fragments.
("Suboptimal" orientations are also seen for some other coordinations).
Solid Builder
Quartz, SiO
2, classified as "ionic" instead of network-covalent.
Solid Builder
Retrieval of the quartz structure, SiO
2, causes program crash.
Builder "Sólido" (ODYSSEY Español)
The diacritical marks for the structure type names are displayed incorrectly.
Builder "Sólido" (ODYSSEY Español)
The diacritical marks for the structure type names have been deliberately omitted.
Builder "Sólido" (ODYSSEY Español)
In the list of "Molecular" structures, the model of solid sulfur is empty
(causes one-time error on opening the panel).
Simulation of Liquids with Molecules of More Than 15 Atoms
User-built liquids and solutions that contain molecules with more than 15 atoms
will not always be treated correctly in simulations that
directly follow the building phase.
Remedy: After building, save the model, close it, and reopen it.
Nucleotide Builder
Self-built polynucleotides are not saved correctly; this leads to problems when reopening a saved model.
Speed Distribution / Kinetic Energy Distribution
If a new system is built, its speed distribution
(or kinetic energy distribution) is not available until the model has been saved, closed,
and reopened.
Model Kit Tutorial Pages (Japanese version only)
The Japanese-language pages in the "Building with the Model Kit" section cannot be annotated, i.e.,
the corresponding icon is nonfunctional.
(In their English translations, the same pages can be annotated as usual.)
Organic Builder
Inserting "H" and then clicking on the hydrogen will make the program crash.
Entry-Level/Organic Builder
Inserting "H" and then clicking on the hydrogen will make the program crash.
Builder "Básico" (ODYSSEY Español)
Inserting "H" and then clicking on the hydrogen will make the program crash.
Entry-Level Builder
Inserting "H" and then clicking on the hydrogen will make the program crash.
Molecule/Ion or Organic Builder
Trying to attach a (noble gas-style) zero-valence atom to a free valence makes the program crash.
Functionality, Platforms, Licensing
Right-Click Menu when an Atom is Selected (Windows version only)
If an atom has been selected, the first item of the right-click (contextual) menu
is erroneously labeled as "Select Atom-4" instead of "Select Atom". (However, the functionality is unaffected: Selecting
the item invokes the "Select Atom" mode.)
Visualization of Collisions
The
Collisions visualization does not work for chain-like molecules
(propane and up, similar inorganic molecules are also affected) because multiple halos are permanently drawn for
each molecule.
Saving Models (Macintosh version only)
Saving a model ("File
Save As") causes the program to crash if the model's title
(shown in the drop-down menu in the upper left corner) contains the ">" or "<" symbols.
This is typically the case if the model's title includes some temperature information.
WORD Formatted Worksheets (Japanese Instructor's Edition only)
The hyperlinks to the WORD formatted worksheets at the bottom of worksheet pages are inoperative.
Remedy: Directly open the corresponding WORD files in the "worksheets WORD, EDITABLE" and "worksheets WORD, READ-ONLY" subfolders
(to be found in the main
ODYSSEY installation folder).
Composition of Models with Monatomics
For models with monatomic particles only (e.g., metals and the noble gases),
the composition (
Properties: "Composition
Number of Atoms") cannot be changed (neither by editing the property field nor
by changing the position of slider).
DHTML Scripting
Can't run on FAT32 file systems (incorrect file sorting leads to script errors)
Models with Multiple Monatomic Particles
If a model contains two or more monoatomic particles, a missing pair interaction
may sometimes lead to a spurious overlap between those particles and physically strange results.
(This problem also affects the following substances in the Molecular Stockroom:
Ag, Al, Ar, Au, Be, Co, Cu, Fe, He, Kr, Ne, Ni, Pb, Pd, Pt, Th, Ti, Xe, and Zn.)
Property Measurements (Macintosh version only)
The selection mechanism for atoms and molecules may get into a hung state if there is some switching between tabs
and
more than one property is being queried.
Dipole Moment Calculation
Sometimes incorrect
Molecular Charges of Complexes
The values displayed in the "Properties" table are incorrect.
Absolute Temperature (Macintosh version only)
When the temperature unit in
Preferences is set to "K", the unit displayed in the
Properties table should be "K" rather than "°K".
Enthalpy of Diatomic Gases
Value is not the standard enthalpy.
Enthalpy of Monatomic Gases
Value for monoatomic gases is not the standard enthalpy, for some cases (1.0, 1.1) or for all cases (1.2).
Entropy
Value for diatomic gases (when available) is wrong after a
volume change
Free Energy
Incorrect calculation
Heat Bath Coupling
Bug affected
Instantaneous Pressure of Gas Samples Prior to Simulation
The instantaneous pressure displayed immediately after page load
(or after building a new sample of gas with the Cell build panel) is incorrect.
Molar Mass Calculation
Incorrect for some large biomolecules (e.g., for "DNA Strand")
Molecular Surface Area Calculation
Systematically imprecise
Molecular Volume Calculation
Systematically imprecise
Pair Distribution Function (Instructor's Edition only)
x-axis of g(r) mislabeled (nm instead of A) (Expert Mode)
Potential Energy Calculation
Incorrect for molecules with 1-4 charge interactions
Translational Temperature (Instructor's Edition only)
Incorrect in some cases (Expert Mode)
Rotational Temperature (Instructor's Edition only)
Incorrect in some cases (Expert Mode)
Integration Time Step (Macintosh Instructor's Edition only)
The unit is missing from the "Dynamics
Integration Time Step" property
(
Expert mode only). The unit is "fs" (femtoseconds, 10
15 sec).
Annotation of Stockroom Pages (Windows version only)
The following pages in the Molecular Stockroom cannot be successfully annotated:
Cholesterol in Trichloromethane;
DMSO-Water; Methanol-Ethanamide; Titan Atmosphere;
(Mixtures) With DMF; (Mixtures) With Propanone;
DMF-Pentane; Octanol-Water;
1,2-Dichloroethene; Amino Acids; Chlorinated Ethanoic Acid;
PETE; PVC; Polyethene; Polypropene
Opening Pages with Multiple and Complex Molecular Models (Windows version only)
On certain relatively slow machines, the message box titled "Open" (confirms the initialization of the various models) may not always close properly on completion of the page load.
Remedy: Reload the page.
"Spinner" for Changing the Number of Molecules
The spinner functionality (up/down arrows) of the "Number-of-Molecules" slider is inoperable.
(however, the horizontal slider works correctly)
Using SPARTAN ST as a Calculation Tool for ODYSSEY Models (SPARTAN ST for Windows only)
All versions of
SPARTAN will open
ODYSSEY-generated models without problems if they were saved in
the
.odydata file format. However, in the Windows version of
SPARTAN Student Edition (the other versions are not affected) an "Unsupported" message may be displayed
if a calculation is set up with the
Calculations dialog.
Remedy: Open the
.odydata file. The first line contains "keywords"add the following
keyword at the end of the line: MMFF.
Using SPARTAN as a Building Tool
When building systems (
SPARTAN
ODYSSEY), the first component must be
entirely built prior to the second component,
the second component
entirely built prior to the third component, etc.
Velocity Initialization
Bug affected
Visualization of Double and Triple Bonds with "Ball and Spoke" Style
Bonds not always properly "oriented"
Page Reload of Experiments
The mouse-over "tool tip" for the Reload button says "Reload First Page of this Topic" even though
the reload takes the user back to the
current (not necessarily first) page.
Saving of Models with Ribbons as .odydata files
Saving of models with ribbon representations in the
.odydata format leads to program crash.
(The
.xodydata format works fine.)
Recording Plots with Number Editing of the Variables (Macintosh version only)
When a snap plot is generated and the independent variable is changed by
editing the corresponding
number field (as opposed to using the adjacent slider), the
Record button may become inoperative:
no new datapoint is generated after clicking on the button even though it is "lighted up".
Remedy: Click on the model background once, then reselect the Record button.
Snap Plots with Long Lists of Properties (Windows version only)
Incorrect values will be recorded if many properties (more than ~10) have been added to the list.
Printing Snapshots of Models (Windows version only)
Snapshots of models will not print correctly if the Properties table is shown and a property
is "active", i.e., selected (indicated by a blue background behind the property name).
No problems occur if all properties are inactive
( = none is selected).
Saving Images in the 'JPG' Format
Will erroneously save in the 'BMP' format if a filename is declared (but works correctly if the default filename is accepted)
© 2004-2008 Wavefunction, Inc.