Tutorial on YouTube (mobile devices)
Click here to try out Arrows by sending it an email
Are you just learning NWChem and would like to have an easy way to generate input decks, check your output decks against a large database of calculations, perform simple thermochemistry calculations, calculate the NMR and IR spectra of modest size molecule, or just try out NWChem before installing it? EMSL Arrows scientific service can help. A Web API to EMSL Arrows is now available for Alpha testing. Click on this [link](https://arrows.emsl.pnnl.gov/api). For more information contact [Eric Bylaska (eric.bylaska@pnnl.gov)](mailto:eric.bylaska@pnnl.gov?Subject=EMSL%20Arrows%20Question) [* EMSL Arrows API*](https://arrows.emsl.pnnl.gov/api) The difficulty of simulating the thermodynamic and kinetic properties of new materials is convoluted by the sensitivity of the processes at the macroscopic scale to the atomic scale; the unusual and unexpected bonding behaviors of the materials; the complex extreme temperature and pressure environments likely to be encountered; and the requirements that simulations be as parameter free as possible and extremely reliable. The tools of quantum chemistry and statistical mechanics combined with advanced parallel packages such as NWChem have proved to be very effective and productive. Not surprisingly, programs that implement these types of tools make up a large fraction of DOE OS supercomputer cycles. Despite these hugely successful theoretical developments, reliable calculations of this type require considerable computational effort and often the use of codes with difficult input decks. The NWChem molecular modeling software implements a robust and diverse set of molecular theories that can estimate the thermodynamics and kinetics of molecules and materials. It arguably has the most capabilities of any molecular modeling code today. The problem with NWChem and other molecular modeling codes is that: - Molecular modeling software is extremely complex, contains millions of lines of code, and takes a long time to set up and to learn how to use. - Even the most basic input for molecular modeling software requires the use of other software to generate it. - Because of this complexity people unnaturally identify with codes and molecular theories, and they are hesitant to learn new codes and new molecular simulation techniques. The goal of this project is to provide EMSL users and DOE scientists and engineers with an open-source computational chemistry and materials tool called EMSL Arrows. EMSL Arrows is a software package that combines NWChem, SQL and NOSQL databases, and email (in the future also social networks, e.g. Twitter, Tumblr) that simplifies molecular and materials modeling and makes these modeling capabilities easier to use and more accessible to many scientists and engineers. EMSL Arrows is very simple to use. The user just emails chemical reactions to arrows@emsl.pnnl.gov and then an email is sent back with thermodynamic, reaction pathway (kinetic), spectroscopy, and other results. EMSL Arrows parses the email and then searches the database for the compounds in the reactions. If a compound isn't there, an NWChem calculation is setup and submitted to calculate it. Once the calculation is finished the results are entered into the database and then results are emailed back. This whole process is completely automated. To enter different calculation types (e.g. use pspw theory, or pbe0 exchange correlation functional) the SMILES is appended with keyword{options} tags. An example email is as follows: ``` To: arrows@emsl.pnnl.gov Subject: Calculate isodesmic reactions Arrows:: Reaction: C(Cl)(Cl)(Cl)O + C --> C(Cl)(Cl)Cl + CO :Reaction Reaction: C(Cl)(Cl)(Cl)O + C --> C(Cl)(Cl)Cl + CO ~ theory{pspw} :Reaction Reaction: C(Cl)(Cl)(Cl)S + C --> C(Cl)(Cl)Cl + CS :Reaction Reaction: C(Cl)(Cl)(Cl)S + C --> C(Cl)(Cl)Cl + CS ~ theory{pm3} :Reaction Reaction: TNT + 3 benzene --> toluene + 3 nitrobenzene ~ xc{pbe} :Reaction ::Arrows ``` The results returned by EMSL Arrows are a combination of text and graphical output.  Currently EMSL Arrows is designed to calculate the following for all NWChem theories: - Reaction thermodynamics for molecular systems - Reaction paths for molecular systems - UV-vis, IR, Raman spectra for molecular systems, phonon spectra for materials systems - NMR spectra for molecular and materials systems - EXAFS spectra for molecular and materials systems - Energetics, structures, and band structures of crystals using the Crystal Open Database (COD ) numbers - A variety of datafiles can be returned including XYZ files, CIF files, NWChem output files We envision that as Arrows evolves it will be part of future closed cycles of chemical and materials discovery that requires integrated computational and experimental tools combined with materials synthesis. ## Try out EMSL Arrows by sending the following simple emails to arrows@emsl.pnnl.gov Returns b3lyp/6-311++G(2d,2p) results for the cinnamon flavored molecule. Click here to run this example. ``` ---------------- mailto: arrows@emsl.pnnl.gov ----------------------- Arrows:: molecule: Cinnamaldehyde :molecule ::Arrows ``` Using MP2 to calculate the reaction energy of a hydrolysis reaction for TNT. Click here to run this example. ``` ---------------- mailto: arrows@emsl.pnnl.gov ----------------------- Arrows:: Reaction: cid=8376 + hydroxide --> O=N(=O)c1cc(O)c(c(c1)N(=O)=O)C + nitrite ~ theory{mp2} :Reaction ::Arrows ``` Examples of [isodesmic reaction](Plane-Wave-Density-Functional-Theory#nwpw-tutorial-3-using-isodesmic-reaction-energies-to-estimate-gas-phase-thermodynamics) Click here to to run this example. ``` ---------------- mailto: arrows@emsl.pnnl.gov ----------------------- Arrows:: Reaction: TNT + 3 benzene --> toluene + 3 nitrobenzene ~ theory{mp2} :Reaction Reaction: C(Cl)(Cl)(Cl)O + C --> C(Cl)(Cl)Cl + CO :Reaction Reaction: C(Cl)(Cl)(Cl)O + C --> C(Cl)(Cl)Cl + CO ~ xc{pbe} :Reaction Reaction: C(Cl)(Cl)(Cl)O + C --> C(Cl)(Cl)Cl + CO ~ theory{pspw} :Reaction ::Arrows ``` Examples of reaction prediction capabilities in Arrows. Click here to to run this example. ``` ---------------- mailto: arrows@emsl.pnnl.gov ----------------------- Arrows:: Predict: 2 methane :Predict ::Arrows ``` Click here to to run this example. ``` ---------------- mailto: arrows@emsl.pnnl.gov ----------------------- Arrows:: Predict: TNT + hydroxide :Predict ::Arrows ``` Fetch an NWChem output deck from Arrows. Click here to to run this example. ``` ---------------- mailto: arrows@emsl.pnnl.gov ----------------------- Arrows:: nwoutput: caffeine :nwoutput ::Arrows ``` ## Try out the following web API links (Now Available for Alpha Testing) [EMSL Arrows API v1.0](http://arrows.emsl.pnnl.gov/api/) ## Introduction to ESMILES - How to Change Calculation Theories The combined string, `Molecule_Input keyword1{option1} keyword2{option2} keywordN{optionN}`, is called an `extended smiles` or `esmiles` for short. The `Molecule_Input` can be specified using a variety of formats including a SMILES string, common names, iupac, kegg numbers, cas, pubchem ids, chemspider ids, and InChI strings. The keyword{option} tags are used to enter different calculation types for a molecule, e.g. use pspw theory, ccsd(t), or pbe0 exchange correlation functional. The following are examples of esmiles strings: Plane-Wave DFT calculation using LDA and a cutoff energy=30.0 Ry ``` c1ccccc1 theory{pspw} xc{lda} basis{30.0 Ry} ``` MP2 calculation using 6-31G\* basis set ``` CCO theory{mp2} basis{6-31G*} ``` CCSD(T) calculation of ethanol ``` CCO theory{ccsd(t)} basis{6-31G*} ``` Mopac PM3 calculation of caffeine ``` Caffeine theory{pm3} ``` Aperiodic plane-wave DFT calculation of triplet cabon tetrachloride ``` C(Cl)(Cl)(Cl)Cl mult{3} theory{pspw4} ``` Gas-phase M06-2x/6-31+G\* calculation of benzene ``` benzene theory{dft} xc{m06-2x} solvation_type{none} ``` Equivalent ESMILES for CCSD(T)/6-31G\* calculation of methanol ``` methyl alcohol theory{ccsd(t)} basis{6-31G*} kegg=D02309 theory{ccsd(t)} basis{6-31G*} cas=67-56-1 theory{ccsd(t)} basis{6-31G*} cid=887 theory{ccsd(t)} basis{6-31G*} csid=864 theory{ccsd(t)} basis{6-31G*} InChI=1S/CH4O/c1-2/h2H,1H3 theory{ccsd(t)} basis{6-31G*} ``` The available keywords in and esmiles string are: theory, theory\_property, theory\_base, basis, basis\_property, basis\_base, xc, xc\_property, xc\_base, solvation\_type, charge, mult, xyzdata, geometry\_generation, and calculation\_type. ### ESMILES Options - theory{}, theory\_property{} and theory\_base{} The default theory used is theory{dft}. The following theories are available: ``` - dft -- NWChem Gaussian DFT - pspw -- NWChem Plane-Wave DFT (periodic boundary conditions, Γ point) - pspw4 -- NWChem Plane-Wave DFT (aperiodic boundary conditions) - mp2 -- NWChem MP2 program - ccsd(t) -- NWChem CCSD(T) - pm3 -- Mopac7 PM3 - am1 -- Mopac7 AM1 - mindo -- Mopac7 MINDO - mindo3 -- Mopac7 MINDO3 ``` The theory\_property{} is an optional keyword used to specify the theory used in an nmr calculation, and theory\_base{} is an optional keyword used to specify the theory of the base calculation for an MP2 or CCSD(T) calculation. By default the theory\_property and theory\_base are defined to be the same as theory{}. ### ESMILES Options - basis{}, basis\_property{} and basis\_base{} The default basis used is 6-311++G(2d,2p) for the Gaussian DFT, MP2 and CCSD(T) programs. For plane-wave DFT the default basis or cutoff energy is defined to by 50.0 Hartrees or 100.0 Ry. For Gaussian basis sets any basis set recognized by NWChem can be used, e.g. ``` CCO basis{6-31G*} ``` Other common basis sets can be used such as cc-pvdz, 6-311G, 3-21G, 6-31+G\*. For plane-wave basis sets the cutoff energy can changed by just entering the number in Hartrees or Rydbergs ``` CCO theory{pspw] basis{50.0} CCO theory{pspw} basis{100 Ry} ``` The basis\_property{} is an optional keyword used to specify the basis set used in an nmr calculation, and basis\_base{} is an optional keyword used to specify the basis set of the base calculation for an MP2 or CCSD(T) calculation. By default the basis\_property and basis\_base are defined to be the same as basis{}. ### ESMILES Options - xc{}, xc\_property{} and xc\_base{} Only the Gaussian and plane-wave DFT programs utilize the xc{} keyword. The default exchange correlation functional used is xc{b3lyp}. The following exchange correlation functions are available with the Gaussian DFT and plane-wave DFT programs. ``` - lda -- local density approximation (LDA) of S.J. Vosko, L. Wilk and M. Nusair, Can. J. Phys. 58, 1200 (1980) - pbe -- The gradient corrected exchange correlation function of J.P. Perdew, K. Burke and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996); 78 , 1396 (1997) - blyp -- The gradient corrected exchange correlation function A.D. Becke, Phys. Rev. A 88, 3098 (1988) and C. Lee, W. Yang and R. G. Parr, Phys. Rev. B 37, 785 (1988) - b3lyp -- the hybrid exchange correlation function of A.D. Becke, J. Chem. Phys. 98, 5648 (1993) and C. Lee, W. Yang and R. G. Parr, Phys. Rev. B 37, 785 (1988) - pbe0 -- the hybrid exchange correlation function of C.Adamo and V.Barone, J. Chem. Phys. 110, 6158 (1999) - m06-2x -- the hybrid meta exchange correlation function of Y. Zhao, D. G. Truhlar, J. Chem. Phys. 125, 194101 (2006). Only available in Gaussian DFT program ``` The `xc_property{}` is an optional keyword used to specify the exchange correlation potential used in an nmr calculation, and `xc_base{}` is an optional keyword used to specify the exchange correlation potential of the base calculation for an MP2 or CCSD(T) calculation. By default the `xc_property` and `xc_base` are defined to be the same as `xc{}`. ### ESMILES Options - solvation_type{} The default solvation type is solvation\_type{COSMO}. The following solvation types are available with the Gaussian DFT, MP2 and CCSD(T) programs. ``` - COSMO -- The COSMO solvation model of Klampt and Shuurman (solvent=water) - COSMO-SMD -- The extended Minnesota COSMO solvation model of Cramer et al. (solvent=water) - COSMO-SMD:solvent -- where the solvent keyword is from Table of SMD solvent names below - None -- Gas-phase calculation, no solvation model included in the calculations ``` The available SMD `solvent` keywords are given below: | Keyword | Name | | ----------- | ------------------------------- | | h2o | water (default) | | water | water (default) | | acetacid | acetic acid | | acetone | acetone | | acetntrl | acetonitrile | | acetphen | acetophenone | | aniline | aniline | | anisole | anisole | | benzaldh | benzaldehyde | | benzene | benzene | | benzntrl | benzonitrile | | benzylcl | benzyl chloride | | brisobut | 1-bromo-2-methylpropane | | brbenzen | bromobenzene | | brethane | bromoethane | | bromform | bromoform | | broctane | 1-bromooctane | | brpentan | 1-bromopentane | | brpropa2 | 2-bromopropane | | brpropan | 1-bromopropane | | butanal | butanal | | butacid | butanoic acid | | butanol | 1-butanol | | butanol2 | 2-butanol | | butanone | butanone | | butantrl | butanonitrile | | butile | butyl acetate | | nba | butylamine | | nbutbenz | n-butylbenzene | | sbutbenz | sec-butylbenzene | | tbutbenz | tert-butylbenzene | | cs2 | carbon disulfide | | carbntet | carbon tetrachloride | | clbenzen | chlorobenzene | | secbutcl | sec-butyl chloride | | chcl3 | chloroform | | clhexane | 1-chlorohexane | | clpentan | 1-chloropentane | | clpropan | 1-chloropropane | | ocltolue | o-chlorotoluene | | m-cresol | m-cresol | | o-cresol | o-cresol | | cychexan | cyclohexane | | cychexon | cyclohexanone | | cycpentn | cyclopentane | | cycpntol | cyclopentanol | | cycpnton | cyclopentanone | | declncis | cis-decalin | | declntra | trans-decalin | | declnmix | decalin (cis/trans mixture) | | decane | n-decane | | decanol | 1-decanol | | edb12 | 1,2-dibromoethane | | dibrmetn | dibromomethane | | butyleth | dibutyl ether | | odiclbnz | o-dichlorobenzene | | edc12 | 1,2-dichloroethane | | c12dce | cis-dichloroethylene | | t12dce | trans-dichloroethylene | | dcm | dichloromethane | | ether | diethyl ether | | et2s | diethyl sulfide | | dietamin | diethylamine | | mi | diiodomethane | | dipe | diisopropyl ether | | dmds | dimethyl disulfide | | dmso | dimethyl sulfoxide | | dma | N,N-dimethylacetamide | | cisdmchx | cis-1,2-dimethylcyclohexane | | dmf | N,N-dimethylformamide | | dmepen24 | 2,4-dimethylpentane | | dmepyr24 | 2,4-dimethylpyridine | | dmepyr26 | 2,6-dimethylpyridine | | dioxane | 1,4-dioxane | | phoph | diphenyl ether | | dproamin | dipropylamine | | dodecan | n-dodecane | | meg | 1,2-ethanediol | | etsh | ethanethiol | | ethanol | ethanol | | etoac | ethyl acetate | | etome | ethyl formate | | eb | ethylbenzene | | phenetol | ethyl phenyl ether | | c6h5f | fluorobenzene | | foctane | 1-fluorooctane | | formamid | formamide | | formacid | formic acid | | heptane | n-heptane | | heptanol | 1-heptanol | | heptnon2 | 2-heptanone | | heptnon4 | 4-heptanone | | hexadecn | n-hexadecane | | hexane | n-hexane | | hexnacid | hexanoic acid | | hexanol | 1-hexanol | | hexanon2 | 2-hexanone | | hexene | 1-hexene | | hexyne | 1-hexyne | | c6h5i | iodobenzene | | iobutane | 1-iodobutane | | c2h5i | iodoethane | | iohexdec | 1-iodohexadecane | | ch3i | iodomethane | | iopentan | 1-iodopentane | | iopropan | 1-iodopropane | | cumene | isopropylbenzene | | p-cymene | p-isopropyltoluene | | mesityln | mesitylene | | methanol | methanol | | egme | 2-methoxyethanol | | meacetat | methyl acetate | | mebnzate | methyl benzoate | | mebutate | methyl butanoate | | meformat | methyl formate | | mibk | 4-methyl-2-pentanone | | mepropyl | methyl propanoate | | isobutol | 2-methyl-1-propanol | | terbutol | 2-methyl-2-propanol | | nmeaniln | N-methylaniline | | mecychex | methylcyclohexane | | nmfmixtr | N-methylformamide (E/Z mixture) | | isohexan | 2-methylpentane | | mepyrid2 | 2-methylpyridine | | mepyrid3 | 3-methylpyridine | | mepyrid4 | 4-methylpyridine | | c6h5no2 | nitrobenzene | | c2h5no2 | nitroethane | | ch3no2 | nitromethane | | ntrprop1 | 1-nitropropane | | ntrprop2 | 2-nitropropane | | ontrtolu | o-nitrotoluene | | nonane | n-nonane | | nonanol | 1-nonanol | | nonanone | 5-nonanone | | octane | n-octane | | octanol | 1-octanol | | octanon2 | 2-octanone | | pentdecn | n-pentadecane | | pentanal | pentanal | | npentane | n-pentane | | pentacid | pentanoic acid | | pentanol | 1-pentanol | | pentnon2 | 2-pentanone | | pentnon3 | 3-pentanone | | pentene | 1-pentene | | e2penten | E-2-pentene | | pentacet | pentyl acetate | | pentamin | pentylamine | | pfb | perfluorobenzene | | benzalcl | phenylmethanol | | propanal | propanal | | propacid | propanoic acid | | propanol | 1-propanol | | propnol2 | 2-propanol | | propntrl | propanonitrile | | propenol | 2-propen-1-ol | | propacet | propyl acetate | | propamin | propylamine | | pyridine | pyridine | | c2cl4 | tetrachloroethene | | thf | tetrahydrofuran | | sulfolan | tetrahydrothiophene-S,S-dioxide | | tetralin | tetralin | | thiophen | thiophene | | phsh | thiophenol | | toluene | toluene | | tbp | tributyl phosphate | | tca111 | 1,1,1-trichloroethane | | tca112 | 1,1,2-trichloroethane | | tce | trichloroethene | | et3n | triethylamine | | tfe222 | 2,2,2-trifluoroethanol | | tmben124 | 1,2,4-trimethylbenzene | | isoctane | 2,2,4-trimethylpentane | | undecane | n-undecane | | m-xylene | m-xylene | | o-xylene | o-xylene | | p-xylene | p-xylene | | xylenemx | xylene (mixture) | When a solvent is specified by name, the descriptors for the solvent are based on the Minnesota Solvent Descriptor Database: Winget, P.; Dolney, D. M.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. Minnesota Solvent Descriptor Database. University of Minnesota: Minneapolis, MN, 2010.