## Sunday, January 27, 2013

### Peer instruction question on enthalpy

Is this an endo- or exothermic process?

## Saturday, January 26, 2013

### Where to submit your research paper?

Jeremy Fox wrote an interesting blog post, which in turn has sparked at least two others (here and here).  Here are my thoughts on the issues that were raised, though taken in a different order, plus a few extra questions at the end.

Aim as high as you reasonably can.  As I read it the main point made in the original post is: don't waste time submitting to journals where the paper has very little chance of getting accepted.  I agree with this.

I've come to the opinion that for me (a computational chemist) the journal landscape has three tiers:
1. Science and Nature (I have never submitted a paper there)
2. Journals with an impact factor greater than roughly 10 (PNAS, JACS, etc).  (I submit once in a blue moon.)
3. Everything else.  (This is were the vast majority of my papers go).

Is it a society journal?  For Tier 3 journals my preferences are PLoS ONE >> society journals > commercial publishers (with Elsevier dead last).

I'm not particularly excitable but the Research Work Act really "brought my pis to a boil" as they say here in Denmark.  The RWA made me realize that commercial publishers (who lobbied hard for this piece of ... legislation) view my papers as their property (which it is once you sign away your copyright!) and are willing to actively hurt science to increase their already obscene profits.  So I joined the Elsevier boycott.

However, it is worth remembering that the RWA was "applauded" by the Association of American Publishers which includes societies such as the ACS and AIP.  To their credit AIP (which publishes JCP), AAAS (Science), NPG (Nature, Nature Chem) came out and opposed the RWA. Eventually, the ACS also kinda-sorta did but only after the RWA became so unpopular that Elsevier dropped its support (Seriously ACS? After Elsevier? ).

Note also that these societies still charge universities exorbitant prices for their journals (see also this and this) and generate such profits that they are able to shrug off a multimillion dollar loss due to a botched lawsuit against a small rival.

The societies themselves may be not-for-profit outfits, but their publishing divisions certainly are not.

Is the journal open access?  That's a necessary but not sufficient condition.  Consider the BMC journals. Yes, they are OA but they are published by a commercial publisher (Springer) whose mission is to maximise profits.  For example, they are not above selling your figures for profit.  Furthermore, they would not run the OA journal if it did not generate a profit - money they could well use to lobby for the next incarnation of RWA.

That's why I choose PLoS ONE.

For all FMO calculations we used the default values for cutoffs based on distances (RESDIM=2.0 in \$FMO for dimers, RITRIM(1)=1.24, -1.0, 2.0, 2.0 in \$FMO for trimers). To obtain approximate dimer MO coefficients we used MODORB=3 in $FMOPRP. All other setting were default value unless specified directly. ### 3 Results TODO: Compile the results and write about them. Benchmarking water clusters from previous FMO applications should be OK. TODO: There is a problem with the test-systems of the ALA-helices and sheets, perhaps it is because they are too simple and repetitive to actually mean anything #### 3.1 Overlap vs. Distance #### 3.2 Dimers #### 3.3 Trimers ### 4 Conclusion and Outlook 1) there is a noticeble difference between using basis sets with and without diffuse functions 2) works great for molecular clusters, systems with covalent bonds?? ## Wednesday, January 16, 2013 ### Generating an Orthonormal Basis So you have a vector$\mathbf{V}_1=(V_x, V_y, V_z)$and you want to construct an orthonormal basis with that one vector as one of the basis vectors.$\mathbf{V}_1$is not normalized, yet. Here is how I did it, first concentrating on providing the orthogonal set of vectors ### The Orthogonal Basis The first orthorgonal vector to$\mathbf{V}_1$, called$\mathbf{V}_1$is done by $$\mathbf{V}_2=(-V_y, V_x, 0).$$ We can easily verify that$\mathbf{V}_1$and$\mathbf{V}_2$are orthogonal by taking the inner product $$\langle\mathbf{V}_1,\mathbf{V}_2\rangle = V_x\cdot(-V_y)+V_y\cdot V_x + V_z\cdot 0 = -V_xV_y+V_xV_y = 0.$$ The last orthogonal vector$\mathbf{V}_3$is created by taking the cross-product of$\mathbf{V}_1$and$\mathbf{V}_2$yielding $$\mathbf{V}_3=\mathbf{V}_1\times\mathbf{V}_2=(V_y\cdot 0 - V_z\cdot V_x,V_z\cdot (-V_y)-V_x\cdot 0,V_x\cdot V_x - V_y\cdot (-V_y)),$$ and can be reduced to $$\mathbf{V}_3=(-V_x\cdot V_z, -V_y\cdot V_z, V^2_x+V^2_y).$$ Thus$\mathbf{V}_1$,$\mathbf{V}_2$and$\mathbf{V}_3$now constitue an orthogonal basis. However, normalizing by brute-force is cumbersome (and error prone) so we will take a slightly more clever route. ### The Orthonormal Basis If we instead assume that the vector$\mathbf{V}_1$is normalized initially, we have that $$\hat{\mathbf{V}}_1 = (V_x, V_y, V_z).$$ I've re-used the same symbols as before to reduce an unnecessary cluttering of the notation, but do remember that elements of$\hat{\mathbf{V}}_1$are normalized. To help us later on, we can write the length of$\hat{\mathbf{V}}_1$as $$1=\sqrt{V^2_x + V^2_y + V^2_z}=> 1=V^2_x + V^2_y + V^2_z$$ which we will use momentarily.$\hat{\mathbf{V}}_2$is constructed as above but we have to normalize right away $$\hat{\mathbf{V}}_2 = (\frac{-V_y}{\sqrt{V^2_x + V^2_y}}, \frac{V_x}{\sqrt{V^2_x + V^2_y}}, 0)=(\frac{-V_y}{\sqrt{1-V^2_z}}, \frac{V_x}{\sqrt{1-V^2_z}}, 0)$$ In the final equality sign, we used the length of$\hat{\mathbf{V}}_1$. Now, for the cross-product. Remember that the no normalization for$\hat{\mathbf{V}}_3$is needed because$\hat{\mathbf{V}}_1$and$\hat{\mathbf{V}}_2$are already normalized $$\hat{\mathbf{V}}_3=\hat{\mathbf{V}}_1\times\hat{\mathbf{V}}_2=(\frac{-V_z\cdot V_x}{\sqrt{1-V^2_z}},\frac{-V_z\cdot V_y}{\sqrt{1-V^2_z}},\frac{V^2_x+V^2_y}{\sqrt{1-V^2_z}}).$$ The last element of the$\hat{\mathbf{V}}_3$vector is something we can take care of and make it a tad prettier. By using the length of vector$\hat{\mathbf{V}}_1$again we obtain $$\hat{\mathbf{V}}_3=(\frac{-V_z\cdot V_x}{\sqrt{1-V^2_z}},\frac{-V_z\cdot V_y}{\sqrt{1-V^2_z}},\frac{1-V^2_z}{\sqrt{1-V^2_z}}),$$ and if we remember that$x/\sqrt(x)=\sqrt(x)$we finally obtain$\hat{\mathbf{V}}_3$as $$\hat{\mathbf{V}}_3=(\frac{-V_z\cdot V_x}{\sqrt{1-V^2_z}},\frac{-V_z\cdot V_y}{\sqrt{1-V^2_z}},\sqrt{1-V^2_z}).$$ So to sum up, given a normalized vector$\hat{\mathbf{V}}_1$, we can construct an orthonormal basis using the following equations $$\hat{\mathbf{V}}_1 = (V_x, V_y, V_z),$$ $$\hat{\mathbf{V}}_2 =(\frac{-V_y}{\sqrt{1-V^2_z}}, \frac{V_x}{\sqrt{1-V^2_z}}, 0),$$ $$\hat{\mathbf{V}}_3=(\frac{-V_z\cdot V_x}{\sqrt{1-V^2_z}},\frac{-V_z\cdot V_y}{\sqrt{1-V^2_z}},\sqrt{1-V^2_z}).$$ The clever thing about these last expressions is that the normalization factor$\sqrt{1-V^2_z}$is present many times and can be precomputed for each new$\hat{\mathbf{V}}_1$. Acknowledgements: Thanks to Lars for being awesome with the math. ### Manuscript review: Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry +Casper Steinmann's latest paper, which he submitted to PLoS ONE late last month, has already been reviewed! Way to go PLoS ONE! Points 1-6 are easily addressed. 7. cc-pVTZ single points on one representative path should be no problem, even with MP2. If we see only a small change in barrier I would argue against cc-pVQZ calculations. Otherwise, we should at least do the B3LYP/cc-pVQZ calculations on the same path. 8. I don't quite follow the line and page number reference. But we use a smaller model than Claeyssens et al.: all atoms with 16 Å and 25 Å of the active site, respectively. So the enzyme model is poorer. 9. Of course the reaction enthalpy in the enzyme cannot be measured, only estimated, so it's not a good benchmark. Nevertheless, Claeyssens et al. estimate the "experimental" enzymatic reaction enthalpy to be between -15 and -13 kcal/mol. Our best prediction of the reaction enthalpy is about -6 kcal/mol (Figure 6). Reference 37 predicts between -26 and -36 kcal/mol (and Claeyssens et al. -18.2$\pm$1.3 kcal/mol). Clearly the predictions differ greatly, but the problem seems to lie more with the method described in reference 37. 10. I think that should actually be 5.4 kcal/mol (27.6-22.2) instead of 8. Anyway, the main change is the inclusion of enzyme-substrate dispersion interactions, which must be weaker in the TS compared to the reactant. It is not clear whether the largest effect is on the H-bonds to the substrate or a many small contributions from all the atoms in the blue and red region in Figure 4. Additional calculations would be required, I don't think it's worth it. 11. Claeyssens et al. (reference 40 in our paper) computed the barrier with B3LYP/6-31G(d). 12. As we write on page 10: our barrier is 18.3$\pm$3.6 kcal/mol and Claeyssens et al.'s barrier is 9.7$\pm$1.8 kcal/mol. 13. As mentioned on page 10: The experimental activation enthalpy is 12.7$\pm$0.4 kcal/mol. So Claeyssens et al.'s error is 3.0 kcal/mol and our error is 5.5 kcal/mol. The multilayer barrier represents just one MD snapshot. 14. This has been addressed in point 9. From: PLOS ONE <plosone@plos.org> Date: 14. jan. 2013 20.56.05 CET To: Casper Steinmann <xxx> Subject: PLOS ONE Decision: Revise [PONE-D-12-39084] PONE-D-12-39084 Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: towards all ab initio Biochemistry PLOS ONE Dear Mr Steinmann, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit, but is not suitable for publication as it currently stands. Therefore, my decision is "Major Revision." We invite you to submit a revised version of the manuscript that addresses the points below: There are some minor issues listed below, but one primary problem that must be addressed with additional text and possibly the single point calculations that the referee refers to in point 7. The serious energy discrepancy must be addressed as amply discussed by the reviewer. We encourage you to submit your revision within forty-five days of the date of this decision. When your files are ready, please submit your revision by logging on tohttp://pone.edmgr.com/ and following the Submissions Needing Revision link. Do not submit a revised manuscript as a new submission. Before uploading, you should proofread your manuscript very closely for mistakes and grammatical errors. Should your manuscript be accepted for publication, you may not have another chance to make corrections as we do not offer pre-publication proofs. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Please also include a rebuttal letter that responds to each point brought up by the academic editor and reviewer(s). This letter should be uploaded as a Response to Reviewers file. In addition, please provide a marked-up copy of the changes made from the previous article file as a Manuscript with Tracked Changes file. This can be done using 'track changes' in programs such as MS Word and/or highlighting any changes in the new document. If you choose not to submit a revision, please notify us. Yours sincerely, xxxx Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Please explain (optional). Reviewer #1: (No Response) 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Please explain (optional). Reviewer #1: (No Response) 3. Does the manuscript adhere to standards in this field for data availability? Authors must follow field-specific standards for data deposition in publicly available resources and should include accession numbers in the manuscript when relevant. The manuscript should explain what steps have been taken to make data available, particularly in cases where the data cannot be publicly deposited. Reviewer #1: Yes Please explain (optional). Reviewer #1: (No Response) 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors below. Reviewer #1: Yes Please explain (optional). Reviewer #1: (No Response) 5. Additional Comments to the Author (optional) Please offer any additional comments here, including concerns about dual publicationor research or publication ethics. Reviewer #1: This paper describes the implementation and first tests of the frozen-domain approximation for the effective fragment molecular orbital method for the chorismate mutase enzyme reaction. The calculations are carefully tested and well done. The results are interesting and therefore publishable. However, compared to previous calculations, the approach shows very large deviations in some energies. These need to be explained before the method can be trusted (points 9 and 10). 1. The level of EFMO should be specified in the abstract. 2. It should be shortly discussed how dangling bonds in the QM calculations are treated. 3. The protonation of all residues should be specified, in particular for the His residues. The number of counter ions and their nature (what element?) should also be specified. 4. I suppose Bohr should also be written with a capital B. 5. The legend of Figure 3 should point out that C1 and C5 is the shared atom. 6. I suppose the references to Figure 2 on p. 6 are misprints (should be Figures 4 and 5). 7. Single-point calculations should also be performed for isolated chorismate with TZP and QZP basis sets, both at B3LYP and MP2 levels of theory, to check the basis set effects. 8. Line -5 on p. 9: Is the enzyme model poorer in the present or the previous study? 9. The ~30 kcal/mol difference in the reaction energy between the present results and those in refs 36 and 37 is very alarming. It sounds unlikely that this should be caused by the restricted relaxation in this study (the large model changes the energy by only 3 kcal). This difference must be better explained. How could the authors expect that we should trust a method that can give errors of 30 kcal? 10. Why do the multilayer calculations give so different results (8 kcal) compared to the ONIOM calculations? Which approach is best? Again, this large difference is very alarming and reduces the credibility of the present approach. 11. Still another reason for the difference between the present results and that by Claeyssens et al. is of course the use of LCCSD(T0) with large basis sets in the latter study. 12. Is the energy spread among the 7 snapshots similar or larger than in previous studies? 13. I cannot see that a doubling of the computational cost is a big problem. On the other hand, in my eyes a method that gives errors of 30 kcal, or even 8 kcal is completely useless. The authors should think more on the accuracy than on the timing. 14. Is the reaction enthalpy experimentally known? It seems to be harder to estimate than the activation enthalpy and therefore more interesting to study and reproduce. 6. If you would like your identity to be revealed to the authors, please include your name here (optional). Your name and review will not be published with the manuscript. Reviewer #1: (No Response) ## Tuesday, January 8, 2013 ### Summary of select research projects Summary of Select Research Project (Early 2013) from molmodbasics Yesterday I made a presentation at at group meeting of the Stamou Group and briefly described three projects that might be of interest to them: projects by +Casper Steinmann+Anders Steen Christensen, and +Martin Hediger This work is licensed under a Creative Commons Attribution 3.0 Unported License. ## Saturday, January 5, 2013 ### Negative temperature: the equations A recent Science paper entitled Negative Absolute Temperature for Motional Degrees of Freedom has generated a lot of discussion on the blogosphere (example) already. This post is about the equations behind the concept of negative temperature. The discussion and figure is taken out of chapter 12 of the excellent book Thermodynamic Driving Forces by Dill and Bromberg. The thermodynamic definition of temperature is $$dS=\frac{dU}{T}=\left(\frac{dS}{dU}\right)_{V,N}dU\Rightarrow\frac{1}{T}=\left(\frac{dS}{dU}\right)_{V,N}$$while the statistical mechanical definition of entropy is $$S=k\ln(W)$$ For a two-state system (Figure 12.1)$$\frac{1}{T}=k\left(\frac{d\ln(W)}{dn}\right)_{V,N} \left(\frac{dn}{dU}\right)$$The multiplicity term can be rewritten as $$\ln(W)=\ln\left(\frac{N!}{n!(N-n)!}\right)\approx-n\ln\left(\frac{n}{N}\right)-(N-n)\ln\left(\frac{N-n}{N}\right)$$where the last term used Stirling's approximation$x!\approx (x/e)^x$. The internal energy is given by$$U=n\varepsilon_0\Rightarrow\frac{dn}{dU}=\frac{1}{\varepsilon_0}$$so$T$can be defined in terms of the fraction of molecules in the ground$(f_{ground}=n/N)$and excited state$(f_{excited}=1-n/N)$$$\frac{1}{T}=\frac{k}{\varepsilon_0}\ln\left(\frac{f_{ground}}{f_{excited}}\right)$$At equilibrium these fractions are determined by the Boltzmann distribution$$\frac{f_{ground}}{f_{excited}}=e^{\varepsilon_0/kT}>1$$This is the$T$you measure with a thermometer and this$T$can never be negative at equilibrium. However, if you create a excited macrostate for which$f_{ground}/f_{excited}<1$then the corresponding variable$T$can indeed be negative. As pointed out by Michael de Podesta this happens all the time in a laser. This work (except the first figure which is © by Garland Science) is licensed under a Creative Commons Attribution 3.0 Unported License. ### Journal of Molecular Modeling considers manuscripts deposited on arXiv From: Jan Halborg Jensen Sent: Thursday, January 03, 2013 2:22 PM To: Journal of Molecular Modeling Subject: Re: Manuscript JMMO-D-12-xxx for review Dear xxx Happy new year! Does JMMO consider paper that have been deposited on the preprint server arXiv? I ask because I am boycotting (i.e. not reviewing for or submitting to) all journals that don't. Best regards, Jan ---- From: xxx Sent: Friday, January 04, 2013 9:02 AM To: Jan Halborg Jensen; xxx Subject: JMM Dear Jan, I confirm that JMM consider archived papers. Regards. xx ---- From: Jan Halborg Jensen Sent: Friday, January 04, 2013 10:28 AM To: xxx Subject: Re: JMM Dear xxx Excellent! Then I'd be happy to review the paper. Best regards, Jan This work is licensed under a Creative Commons Attribution 3.0 Unported License. ## Wednesday, January 2, 2013 ### Manuscript in progress: Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics +Anders Steen Christensen and I are working on the first draft of this manuscript. Here is the story as I see it now (stay tuned for updates). The ProCS method We introduce the QM-based ProCS method for predicting backbone amide proton chemical shifts given a protein structure. It is a generalization and improvement of a method I published earlier. Reproducing QM chemical shifts ProCS is parameterized based on B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d) calculations. This level of theory has been shown to yield reliable proton chemical shifts (how reliable for small molecules). ProCS involves several terms from backbone dihedral angles, hydrogen bonding, etc. with an additivity assumption. If everything works perfectly we should be able to reproduce B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d) chemical shifts for a protein structure. Anders has computed the B3LYP/6-311G(d,p)/PCM chemical shielding tensors for the 1ET1 x-ray structure. (The lack of diffuse functions is taken care of by scaling factor from literature). ProCS can reproduce QM with an RMSD of 0.37 ppm. Remaining deviation must come from non-additivity. The empirical methods do not agree well with the DFT results. The DFT CSs span a relatively large range while the empirically predicted CSs span a very short range. This indicates that the empirical methods are less sensitive to small differences in hydrogen bond geometry. Reproducing experimental chemical shifts from X-ray structures QM reproduces small molecule H1-CSs with RMSD of xx. However, for 1ET1 the RMSD is yy. The main source of the discrepancy are likely inaccuracies in the x-ray structure HB-bond lengths since there is an exponential dependence. The PROCS RMSD (0.63) is similar to the QM RMSD(??), and significantly larger than the RMSD between QM and ProCS, indicating that ProCS sufficiently accurate. Going to 13 other proteins the RMSD for ProCS is double that of 1ET1, because more amide protons not involved in HBs. The RMSDs for the empirical methods are significantly smaller than ProCS. This is also found for 13 other X-ray structures. This is because the empirical methods are parameterized using x-ray structures. In order for these methods to produce low RMSD relative to experiment they need to be insensitive to errors in protein structure. Monte-Carlo implementation of protein structure refinement based on chemical shifts Why MC? No gradients for ProCS. More efficient sampling based on Bayesian inference. Anything else? Refining protein structures based on chemical shifts We refine the structure of three proteins each based on three energy function: OPLS alone, OPLS+ProCS and OPLS+Camshift. The MC-refinement of a protein structure results in an ensemble of X (?) protein structures from which average chemical shifts for each amide proton are computed. These average ProCS chemical shifts are in better agreement with experiment compared to using x-ray. The hydrogen bond geometries in the ensemble are very close to the x-ray structures. These average Camshift chemical shifts are in not in better agreement with experiment compared to using x-ray. The hydrogen bond geometries in the ensemble are longer than in the x-ray structures. This is because OPLS prefers longer bond lengths. Trans-hydrogen bond coupling constants Better agreement with x-ray structures does nto necessarily imply better solution-phase structures, so we computed average trans-hydrogen bond coupling constants and compared to experiment. The coupling constants based on the Pro-CS refined ensembles are indeed in better agreement with experimental values indicating the refinement led to improved hydrogen bond geometries Summary ProCS is a QM-based backbone amide proton chemical shift predictor that can deliver QM quality CS predictions for a protein structure in less than a second. Agreement with experiment is worse compared to empirically predicted CS, but we show that this is because empirical CS predictors are insensitive to small errors in hydrogen bond geometry in the x-ray structures. This is because they are parameterized using such x-ray structures. The agreement between ProCS CSs and experiment can be improved by refining the protein structure using an energy function that includes a force field term and a CS term. This also results in better predicted trans-hydrogen bond coupling constants indicating that the refined protein structures indeed have improved. A similar refinement using Camshift CS lead to worse protein structure by the same criterion. Empirical CS-predictors result CSs that agree better with experiment. However, they are relatively insensitive to protein structure and are therefore not suitable for protein structure refinement. This work is licensed under a Creative Commons Attribution 3.0 Unported License ## Tuesday, January 1, 2013 ### The enthalpy increases when bonds are broken Enthalpy changes comes mainly from changes in bonding An enthalpy change has four contributions$$\Delta H^\circ=\Delta E^{Molecular}+\Delta H^{\circ,Translation}+\Delta H^{Rotation}+\Delta H^{Vibration}$$The molecular energy$\Delta E^{Molecular}$is associated with the electrons and nuclei, i.e. chemical and intermolecular bonding, and this is often the largest term. For example for the reaction$H_2 \rightarrow 2H$the enthalpy contributions are:$$\Delta H^\circ = 460.2+6.3-2.5-26.4=437.6 \text{ kJ/mol}$$For breaking the hydrogen bond between two water molecules,$H_2O\cdot \cdot \cdot HOH\rightarrow 2H_2O$, the energy terms are$$\Delta H^\circ = 20.5+6.3+3.8-17.6=13.0 \text{ kJ/mol}$$In both cases$\Delta H^\circ$is positive mainly because it requires energy to break a covalent bond or a hydrogen bond. Figure 1. The attraction between partially charged atoms in a hydrogen bond is contained in$\Delta E^{Molecular}$[image source] Estimating enthalpy changes of chemical reactions Most chemical reactions are not as simple as$H_2 \rightarrow 2H$and involve the making and breaking of several bonds. For example for this reaction there are three double bonds and one single bond in the reactant molecules and one double bond and five single bonds in the product molecule. Figure 2. The prototypical Diels-Alder reaction where 1,3-butadiene reacts with ethene to form cylcohexene To estimate the enthalpy change this reaction you need to know the strengths of CC double and single bonds which are 611 and 347 kJ/mol respectively. So it requires$3\times 611+347=2180$kJ/mol to break the bonds in the reactants and you get back$-(611+5\times 347)=-2346$kJ/mol back when you form the bonds in the products, so$\Delta H^\circ=-166$kJ/mol is a good estimate of the enthalpy change. You can find a list of bond strengths here. The values are given in kcal/mol so you must multiply them by 4.184 to convert to kJ/mol. Enthalpies of formation Enthalpies of formation ($\Delta H^\circ_f$, also called heats of formation) can also be used to estimate$\Delta H^\circ\$ for a reaction.  So for the reaction in Figure 2:$$\Delta H^\circ=\Delta H^\circ_f(\text{cyclobutene})-\Delta H^\circ_f(\text{1,3-butadiene})-\Delta H^\circ_f(\text{ethene})$$ You can find enthalpies of formation of many molecules on the web by Googling or you can estimate them using the Molecule Calculator.

Endothermic and exothermic reactions
Reactions for which the enthalpy increases are called endothermic reactions and reactions for which the enthalpy decreases are called exothermic

Test: Is this an endo- or exothermic process?