Input 1 out of 1
screen lock       

Machine:                    ncpus: queue:            time:   account: None Add Account ──────────     Secret Code: None Add Secret Code ──────────
Arrows queue_name:   QWAIT::      Check submited jobs

Simulation directories

mylabel:

None Add job label ──────────

project name:

model label?

gamma label?

date label?

delete scratch?

curdir0:
permdir:
curdir:

Simulation generation scripts and input

PSPW calculation PSPW4 calculation DFT calculation HF calculation MP2 calculation BAND calculation PSPW-BAND calculation	default def2-svp spherical def2-tzvp spherical 6-31G* cartesian 6-311++G(2d,2p) cartesian 30 Ry 40 Ry 50 Ry 60 Ry 80 Ry 100 Ry 120 Ry	default lda pbe pbe0 singe-pbe0 blyp b3lyp tpss03 scan vs98 m06-2x revpbe pbesol pbe-grimme2 pbe-grimme3 beef xbeef-cpbe beef-vdw2	default Lattice in geometry block Lattice in NWPW block FCC 38 SC 26

water (default) acetic acid acetone acetonitrile acetophenone aniline anisole benzaldehyde benzene benzonitrile benzyl chloride 1-bromo-2-methylpropane bromobenzene bromoethane bromoform 1-bromooctane 1-bromopentane 2-bromopropane 1-bromopropane butanal butanoic acid 1-butanol 2-butanol butanone butanonitrile butyl acetate butylamine n-butylbenzene sec-butylbenzene tert-butylbenzene carbon disulfide carbon tetrachloride chlorobenzene sec-butyl chloride chloroform 1-chlorohexane 1-chloropentane 1-chloropropane o-chlorotoluene m-cresol o-cresol cyclohexane cyclohexanone cyclopentane cyclopentanol cyclopentanone cis-decalin trans-decalin decalin (cis/trans mixture) n-decane 1-decanol 1,2-dibromoethane dibromomethane dibutyl ether o-dichlorobenzene 1,2-dichloroethane cis-dichloroethylene trans-dichloroethylene dichloromethane diethyl ether diethyl sulfide diethylamine diiodomethane diisopropyl ether dimethyl disulfide dimethyl sulfoxide N,N-dimethylacetamide cis-1,2-dimethylcyclohexane N,N-dimethylformamide 2,4-dimethylpentane 2,4-dimethylpyridine 2,6-dimethylpyridine 1,4-dioxane diphenyl ether dipropylamine n-dodecane 1,2-ethanediol ethanethiol ethanol ethyl acetate ethyl formate ethylbenzene ethyl phenyl ether fluorobenzene 1-fluorooctane formamide formic acid n-heptane 1-heptanol 2-heptanone 4-heptanone n-hexadecane n-hexane hexanoic acid 1-hexanol 2-hexanone 1-hexene 1-hexyne iodobenzene 1-iodobutane iodoethane 1-iodohexadecane iodomethane 1-iodopentane 1-iodopropane isopropylbenzene p-isopropyltoluene mesitylene methanol 2-methoxyethanol methyl acetate methyl benzoate methyl butanoate methyl formate 4-methyl-2-pentanone methyl propanoate 2-methyl-1-propanol 2-methyl-2-propanol N-methylaniline methylcyclohexane N-methylformamide (E/Z mixture) 2-methylpentane 2-methylpyridine 3-methylpyridine 4-methylpyridine nitrobenzene nitroethane nitromethane 1-nitropropane 2-nitropropane o-nitrotoluene n-nonane 1-nonanol 5-nonanone n-octane 1-octanol 2-octanone n-pentadecane pentanal n-pentane pentanoic acid 1-pentanol 2-pentanone 3-pentanone 1-pentene E-2-pentene pentyl acetate pentylamine perfluorobenzene phenylmethanol propanal propanoic acid 1-propanol 2-propanol propanonitrile 2-propen-1-ol propyl acetate propylamine pyridine tetrachloroethene tetrahydrofuran tetrahydrothiophene-S,S-dioxide tetralin thiophene thiophenol toluene tributyl phosphate 1,1,1-trichloroethane 1,1,2-trichloroethane trichloroethene triethylamine 2,2,2-trifluoroethanol 1,2,4-trimethylbenzene 2,2,4-trimethylpentane n-undecane m-xylene o-xylene p-xylene xylene (mixture) paw atoms: development_psps psp library HGH_LDA psp library TETER psp library TM psp library pspw_new psp library pspw_old psp library pspw_default psp library :

charge: multiplicity: virtual: Ewald rcut: Ewald ncut: default 1d-slab 2d-hilbert 2d-hcurve np_dimensions: Monkhorst-Pack: dbz(len)_min:

Grassman lmbfgs Grassman cg Stiefel lmfgs Stiefel cg scf loop: scf options: preconditioned block-cg preconditioned cg preconditioned rmm-diis block-cg cg rmm-diis ks_iterations: diis anderson broyden simple density mixing potential mixing ks_alpha: kerker:

Born Model No fractional Fixed fractional Stepped fractional Fermi fractional Gaussian fractional Marzari-Vanderbilt fractional temperature(K): alpha: extra orbitals: No efield periodic efield real space efield APC efield :

translation off rotation off

temperature(K): fake_mass(au): time_step(au): md_loop: total_time(ps): motion_label:

JSMol Builder Options MD_parameters 0 iter. Model 1 out of 1 Polyhedra and Spin Penalty translucent green translucent yellow translucent red translucent blue translucent orange translucent grey up down polyhedra s p d f tetra penta octa other atoms: translucent green translucent yellow translucent red translucent blue translucent orange translucent grey up down polyhedra s p d f tetra penta octa other atoms: translucent green translucent yellow translucent red translucent blue translucent orange translucent grey up down polyhedra s p d f tetra penta octa other atoms: translucent green translucent yellow translucent red translucent blue translucent orange translucent grey up down polyhedra s p d f tetra penta octa other atoms: Reaction Input chemical reaction append: reaction_hash reaction constraint choices reaction constraint reaction_gamma{} reaction_type{ None A + B --> AB AB --> A + B AB + C --> AC + B AB + CD --> CABD CABD --> AB + CD AB + CD --> AD + BC ABCD --> BCA + D EA + BCD --> AB + CDE ABC + DE --> DBE + AC ABCD + E --> A + BC + DE A + BCD + E --> ABC + DE ABCDE --> A + BCD + E A + B + CD --> AC + BD AB + C + D --> CABD AB + C --> ACB ABCD --> DBCA + DC DBCA + DC --> ABCD AB + CD --> ACB + D AC + BD --> A + B + CD ACB --> AB + C ────────── } reaction_indexes{} constraint path input - min_gamma: max_gamma: ngamma: WHAM input - WHAM_spring{} WHAM_gamma{} {} {} WHAM_nsolvent{} posteriori analysis: Auxiliary Penalty Functions npath: Model 1 out of 1 Collective Variable Input Metadynamics TAMD PMF Metadynamics update: print: print_shift: w: sigma: range: nrange: boundary_w: boundary_sigma: tempered: a priori Ebarrier= TAMD update: print: print_shift: gamma: k: mass: ztemp: zinitial: zfixed: range: nrange: PMF coordinate_type{ None bond angle dihedral coord_number group_distance bond_difference2 bondings X Y Z n-plane } atom 1 index (A red): atom 2 index (B green): Reaction: AB --> A + B atom 1 index (red): atom 2 index (green): atom 3 index (blue): atom 1 index (red): atom 2 index (green): atom 3 index (blue): atom 4 index (yellow): atom indexes1: atom indexes2: n12: Sprik: n: R0: m: atom indexes1: atom indexes2: n: coef1 atom1a atom1a coef2 atom2a atom2b ...: atom 1 index (red): atom 1 index (blue): atom 1 index (green): atom 1 index: atom indexes: normal: atom 1 index (A red): atom 2 index (B green): atom 3 index (C blue): Reaction: AB + C --> AC + B f= Lattice Lattice Vectors a1: a2: a3: cell center: Lattice Parameters a: b: c: alpha: beta: gamma: Cartesian Coordinates Fractional Coordinates - locked: Bulk Atoms and Frozen Atoms Bulk-Surface Builders atoms: Simple Cubic Face-Centered Cubic Body-Centered Cubic Tetragonal Body-Centered Tetragonal Hexagonal Closed Packed Rhombohedral Orthorhombic Monoclinic Lattice Diamond Zinc Blende Rock Salt Cesium Choride Fluorite Wurtzite Graphite Graphene lat_a: lat_b: lat_c: c/a: alpha: lat_u: primitive: cubic: a(hkl): b(hkl): c(hkl): SC100 SC001 SC111 FCC100 FCC110 FCC111 FCC211 BCC100 BCC001 BCC110 BCC111 hcp0001 diamond100 diamond111 graphene001 vacuum: origin: scaling: nzplane: tolerance: align c: Interface Builder Base atoms: Simple Cubic Face-Centered Cubic Body-Centered Cubic Tetragonal Body-Centered Tetragonal Hexagonal Closed Packed Rhombohedral Orthorhombic Monoclinic Lattice Diamond Zinc Blende Rock Salt Cesium Choride Fluorite Wurtzite Graphite Graphene lat_a: lat_b: lat_c: c/a: alpha: lat_u: primitive: cubic: a(hkl): b(hkl): c(hkl): SC100 SC001 SC111 FCC100 FCC110 FCC111 FCC211 BCC100 BCC001 BCC110 BCC111 hcp0001 diamond100 diamond111 graphene001 origin: scaling: Adjunct atoms: Simple Cubic Face-Centered Cubic Body-Centered Cubic Tetragonal Body-Centered Tetragonal Hexagonal Closed Packed Rhombohedral Orthorhombic Monoclinic Lattice Diamond Zinc Blende Rock Salt Cesium Choride Fluorite Wurtzite Graphite traphene lat_a: lat_b: lat_c: c/a: alpha: lat_u: primitive: cubic: a(hkl): b(hkl): c(hkl): SC100 SC001 SC111 FCC100 FCC110 FCC111 FCC211 BCC100 BCC001 BCC110 BCC111 hcp0001 diamond100 diamond111 graphene001 origin: scaling: interface distance delta: Thomas Scripting Symmetry Lattice Symmetry symmetry: setting: crystal system: Triclinic Monoclinic Orthorhombic Tetragonal Trigonal Hexagonal Cubic group number: Symmetry Ops +x,+y,+z

Arrows Entry

Enter an esmiles, esmiles reaction, or other Arrows input, then push the "Run Arrows" button.

Calculation Options:

theory/method dft pspw pspw4 mp2 ccsd(t) pm3 band exchange correlation lda pbe pbe0 blyp b3lyp m06-2x scan tpss03 vs98 revpbe pbesol pbe-grimme2 pbe-grimme3 beef xbeef-cpbe beef-vdw2 beef-grimme2 basis sets 6-31G* 6-3111++G(2d,2p) solvation theories gas phase water (COSMO) water (COSMO-SMD) acetic acid acetone acetonitrile acetophenone aniline anisole benzaldehyde benzene benzonitrile benzyl chloride 1-bromo-2-methylpropane bromobenzene bromoethane bromoform 1-bromooctane 1-bromopentane 2-bromopropane 1-bromopropane butanal butanoic acid 1-butanol 2-butanol butanone butanonitrile butyl acetate butylamine n-butylbenzene sec-butylbenzene tert-butylbenzene carbon disulfide carbon tetrachloride chlorobenzene sec-butyl chloride chloroform 1-chlorohexane 1-chloropentane 1-chloropropane o-chlorotoluene m-cresol o-cresol cyclohexane cyclohexanone cyclopentane cyclopentanol cyclopentanone cis-decalin trans-decalin decalin (cis/trans mixture) n-decane 1-decanol 1,2-dibromoethane dibromomethane dibutyl ether o-dichlorobenzene 1,2-dichloroethane cis-dichloroethylene trans-dichloroethylene dichloromethane diethyl ether diethyl sulfide diethylamine diiodomethane diisopropyl ether dimethyl disulfide dimethyl sulfoxide N,N-dimethylacetamide cis-1,2-dimethylcyclohexane N,N-dimethylformamide 2,4-dimethylpentane 2,4-dimethylpyridine 2,6-dimethylpyridine 1,4-dioxane diphenyl ether dipropylamine n-dodecane 1,2-ethanediol ethanethiol ethanol ethyl acetate ethyl formate ethylbenzene ethyl phenyl ether fluorobenzene 1-fluorooctane formamide formic acid n-heptane 1-heptanol 2-heptanone 4-heptanone n-hexadecane n-hexane hexanoic acid 1-hexanol 2-hexanone 1-hexene 1-hexyne iodobenzene 1-iodobutane iodoethane 1-iodohexadecane iodomethane 1-iodopentane 1-iodopropane isopropylbenzene p-isopropyltoluene mesitylene methanol 2-methoxyethanol methyl acetate methyl benzoate methyl butanoate methyl formate 4-methyl-2-pentanone methyl propanoate 2-methyl-1-propanol 2-methyl-2-propanol N-methylaniline methylcyclohexane N-methylformamide (E/Z mixture) 2-methylpentane 2-methylpyridine 3-methylpyridine 4-methylpyridine nitrobenzene nitroethane nitromethane 1-nitropropane 2-nitropropane o-nitrotoluene n-nonane 1-nonanol 5-nonanone n-octane 1-octanol 2-octanone n-pentadecane pentanal n-pentane pentanoic acid 1-pentanol 2-pentanone 3-pentanone 1-pentene E-2-pentene pentyl acetate pentylamine perfluorobenzene phenylmethanol propanal propanoic acid 1-propanol 2-propanol propanonitrile 2-propen-1-ol propyl acetate propylamine pyridine tetrachloroethene tetrahydrofuran tetrahydrothiophene-S,S-dioxide tetralin thiophene thiophenol toluene tributyl phosphate 1,1,1-trichloroethane 1,1,2-trichloroethane trichloroethene triethylamine 2,2,2-trifluoroethanol 1,2,4-trimethylbenzene 2,2,4-trimethylpentane n-undecane m-xylene o-xylene p-xylene xylene (mixture)

The following are examples of input that can be used with Tiny Arrows. Clicking on a button places the command into the above entry box.

Molecular calculations:  

Reaction calculations:  

NMR calculations:  

Predict reactions:  

SMARTS searching:  

Generate NWChem input, Fetch NWChem output, Fetch XYZ and Fetch JSON:  

Other Arrows commands:  

cached notes db (IndexedDB) name:


image to base64
Encode image to base64:

cached table db (IndexedDB) name:

--

table type: Gas-Phase Energy (Hartrees) Gas-Phase Enthalpy (Hartrees) Gas-Phase Free Energy (Hartrees) Solvation Free Energy (Hartrees) Aqueous Free Energy (Hartrees) Gas-Phase Reaction Energy (Hartrees) Gas-Phase Reaction Enthalpy (Hartrees) Gas-Phase Reaction Free Energy (Hartrees) Solvation Reaction Free Energy (Hartrees) Aqueous Reaction Free Energy (Hartrees) HOMO Energy (eV) LUMO Energy (eV) Alpha HOMO Energy (eV) Alpha LUMO Energy (eV) Beta HOMO Energy (eV) Beta LUMO Energy (eV) SubmitEsmiles column theories: }
number table rows:
theory/methods dft pspw pspw4 mp2 ccsd(t) pm3 band exchange correlation lda pbe pbe0 blyp b3lyp m06-2x scan tpss03 basis sets 6-31G* 6-311++G(2d,2p) solvation theories water (COSMO) water (COSMO-SMD) acetic acid acetone acetonitrile acetophenone aniline anisole benzaldehyde benzene benzonitrile benzyl chloride 1-bromo-2-methylpropane bromobenzene bromoethane bromoform 1-bromooctane 1-bromopentane 2-bromopropane 1-bromopropane butanal butanoic acid 1-butanol 2-butanol butanone butanonitrile butyl acetate butylamine n-butylbenzene sec-butylbenzene tert-butylbenzene carbon disulfide carbon tetrachloride chlorobenzene sec-butyl chloride chloroform 1-chlorohexane 1-chloropentane 1-chloropropane o-chlorotoluene m-cresol o-cresol cyclohexane cyclohexanone cyclopentane cyclopentanol cyclopentanone cis-decalin trans-decalin decalin (cis/trans mixture) n-decane 1-decanol 1,2-dibromoethane dibromomethane dibutyl ether o-dichlorobenzene 1,2-dichloroethane cis-dichloroethylene trans-dichloroethylene dichloromethane diethyl ether diethyl sulfide diethylamine diiodomethane diisopropyl ether dimethyl disulfide dimethyl sulfoxide N,N-dimethylacetamide cis-1,2-dimethylcyclohexane N,N-dimethylformamide 2,4-dimethylpentane 2,4-dimethylpyridine 2,6-dimethylpyridine 1,4-dioxane diphenyl ether dipropylamine n-dodecane 1,2-ethanediol ethanethiol ethanol ethyl acetate ethyl formate ethylbenzene ethyl phenyl ether fluorobenzene 1-fluorooctane formamide formic acid n-heptane 1-heptanol 2-heptanone 4-heptanone n-hexadecane n-hexane hexanoic acid 1-hexanol 2-hexanone 1-hexene 1-hexyne iodobenzene 1-iodobutane iodoethane 1-iodohexadecane iodomethane 1-iodopentane 1-iodopropane isopropylbenzene p-isopropyltoluene mesitylene methanol 2-methoxyethanol methyl acetate methyl benzoate methyl butanoate methyl formate 4-methyl-2-pentanone methyl propanoate 2-methyl-1-propanol 2-methyl-2-propanol N-methylaniline methylcyclohexane N-methylformamide (E/Z mixture) 2-methylpentane 2-methylpyridine 3-methylpyridine 4-methylpyridine nitrobenzene nitroethane nitromethane 1-nitropropane 2-nitropropane o-nitrotoluene n-nonane 1-nonanol 5-nonanone n-octane 1-octanol 2-octanone n-pentadecane pentanal n-pentane pentanoic acid 1-pentanol 2-pentanone 3-pentanone 1-pentene E-2-pentene pentyl acetate pentylamine perfluorobenzene phenylmethanol propanal propanoic acid 1-propanol 2-propanol propanonitrile 2-propen-1-ol propyl acetate propylamine pyridine tetrachloroethene tetrahydrofuran tetrahydrothiophene-S,S-dioxide tetralin thiophene thiophenol toluene tributyl phosphate 1,1,1-trichloroethane 1,1,2-trichloroethane trichloroethene triethylamine 2,2,2-trifluoroethanol 1,2,4-trimethylbenzene 2,2,4-trimethylpentane n-undecane m-xylene o-xylene p-xylene xylene (mixture) run options optimizer{cgmin} smear{0.01} smear{0.05} smear{0.1}

Kinetics example with Google Sheets

Encode parsing url

url string :

parsing string:

---

Reaction Prediction

esmiles compounds:
reactants:

max_energy:

max_level:

energy_type:

Erxn(g) Hrxn(g) Grxn(g) Delta_Solvation Grxn(aq)

Reactions

Metabolites

Generated Reactants

This webpage is not finished.

Miscellaneous Commands

• To reset an image use: https://arrows.emsl.pnnl.gov/api/image_reset/11836
• To run multiple reaction cycles use the ncycles tag in predict reaction, e.g. TNT + 2 hydroxide --> ~ ncycles{2}
• To change the accuracy of reaction prediction use the maxlevel tag, e.g. TNT + hydroxide --> ~ maxlevel{2}

Thomas Commands

• Thomas excecute LSD
• Thomas load tylenol
• Thomas run molecule
• Thomas run 2d molecule
• Thomas add water
• Thomas optimize
• Thomas turn on unit cell
• Thomas turn off unit cell
• Thomas center unit cell
• Thomas origin unit cell
• Thomas stick
• Thomas space fill
• Thomas ball and stick
• Thomas 2d
• Thomas 3d
• Thomas switch to 3d builder
• Thomas switch to 2d builder
• Thomas switch to input editor
• Thomas switch to notes
• Thomas switch to spreadsheet
• Thomas switch to output
• Thomas switch to queue
• Thomas switch to instructions
• Thomas toggle builder
• Thomas toggle lattice
• Thomas toggle bulk surface
• Thomas toggle symmetry
• Thomas toggle polyhedra
• Thomas toggle reaction
• Thomas toggle collective

Tiny Arrows is a revolutionary approach to materials and chemical simulations that uses NWChem and chemical computational databases to make materials and chemical modeling accessible via a broad spectrum of digital communications. With this webpage, a molecule can be entered into Tiny Arrows using either an esmiles string, a 2D molecular builder, a 3D molecular builder, or as a NWChem input deck.

ACE: High Performance Code Editor for the Web

JSmol: an open-source HTML5 viewer for chemical structures in 3D

JSME Editor Citation: B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, J. Cheminformatics 5:24 (2013)

Jspreadsheet v4: The javascript spreadsheet

This software service and its documentation were developed at the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory, a multiprogram national laboratory, operated for the U.S. Department of Energy by Battelle under Contract Number DE-AC05-76RL01830. Support for this work was provided by the Department of Energy Office of Biological and Environmental Research, and Department of Defense environmental science and technology program (SERDP). THE SOFTWARE SERVICE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE SERVICE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE SERVICE.

Keywords: quantum chemistry calculations - quantum chemistry computations - quantum chemistry - molecular modeling calculations - molecular modeling computations - molecular modeling - chemical modeling - chemical reactions calculations - chemical reactions computations - chemical reactions - NWChem calculations - computational chemistry - NWChem