Virtual  Molecular  Modeling  Kits:  Playing  Games  with  Quantum  Chemistry  

Nathan  Luehr  Stanford  University  March  27,  2014  

A computational study of novel nitratoxycarbon, nitritocarbonyl, and nitratecompounds and their potential as high energy materials

Robert W. Zoellner a,⇑, Clara L. Lazen b, Kenneth M. Boehr b

a Department of Chemistry, Humboldt State University, One Harpst Street, Arcata, CA 95521-8299, USAb Border Star Montessori School, 6321 Wornall Road, Kansas City, MO 64113-1792, USA

a r t i c l e i n f o

Article history:Received 1 June 2011Received in revised form 22 September 2011Accepted 12 October 2011Available online 22 October 2011

Keywords:NitratoxycarbonNitritocarbonylHigh-energy materialsHartree–FockDensity functional

a b s t r a c t

The Hartree–Fock RHF/6-31G! and density functional B3LYP/6-31G(d) methods were used to determinethe structures and properties of the isomers of the first three members of the series Cn(CO3N)2n+2

(n = 0,1,2). The first member of the series, C0(CO3N)2, has six possible isomers, di(nitrato-O-)acetylene,cis- and trans-di(nitrato-O,O-)ethylene, the novel di(nitrato-O,O,O-)ethane or bis(nitratoxycarbon),di(nitroso)oxalate and the mixed isomer nitroso(nitrato-O,O,O-)acetate. The most stable of these isomers,both at the Hartree–Fock or density functional levels of theory, is di(nitroso)oxalate, followed bynitroso(nitrato-O,O,O-)acetate, and bis(nitratoxycarbon). The electronic energy of the mixed isomer clo-sely approximates the mean of the energies of di(nitroso)oxalate and bis(nitratoxycarbon). Neither thecis- nor the trans-di(nitrato-O,O-)ethylene could be optimized to a stable minimum on the Hartree–Fockor density functional potential energy surfaces, and the di(nitrato-O-)acetylene isomer was a stable min-imum with the Hartree–Fock method but not at the density functional level of theory. Of the two highermembers of the series investigated, Cn(CO3N)2n+2 (n = 1,2), each has two isomers: the nitritocarbonyl-substituted systems — analogous to di(nitroso)oxalate — and the nitratoxycarbon-substituted systems(neglecting mixed isomers containing both nitritocarbonyl and nitratoxycarbon moieties). In these com-pounds, while the nitritocarbonyl derivatives were found to be significantly more stable thermodynam-ically than the nitratoxycarbon derivatives, both systems were stable minima on both potential energysurfaces and may be of interest as high-energy materials.

! 2011 Elsevier B.V. All rights reserved.

1. Introduction

High-energy materials — substances whose characteristics in-clude strained rings and/or cages, high nitrogen contents, and highdensities [1] — often contain nitrogen oxide moieties, such as thenitrocarbons which contain the N-bound nitro group (–NO2).Examples of these molecules include the nitrocubanes [2] andhexanitrobenzene [3]. Other nitrogen oxide substituents onorganic molecules include the N-bound nitroso group (–NO) innitrosocubanes [4] and the mono-O-bound nitroxy group (–ONO2) in nitroxycubanes [1] and pentaerythritol tetranitrate(PETN) [5]. (In the latter case, the nitroxy group is formed throughthe nitration — addition of an NO2 moiety — to the alcohol ratherthan the direct incorporation of a nitroxy group.) The nitroxy moi-ety is more exactly described as an O-bound nitrate group and, assuch, leads to the question of whether a nitrate group can bond to acarbon center with more than one of the nitrate oxygen atoms,such as is illustrated in Fig. 1. Apparently, the nitrato-O,O- andthe nitrato-O,O,O-bonding modes have not yet been observed or

investigated in an organic system. (The novel nitrato-O,O,O-moietyis referred to herein as a nitratoxycarbon substituent for the sake ofnomenclature simplicity and to emphasize that all three of theoxygen atoms in the group are bound to the carbon center.)

Simple organic molecules (essentially alkane, alkene, or alkynederivatives) with nitrate groups bound to a carbon atom may beenvisioned and, if fully substituted, will have the general formulaCn(CO3N)2n+2, where n = 0,1,2,3, and so forth. When n = 0, the iso-meric molecules (1, cis-2, trans-2, 3, 4, and 5) depicted in Fig. 2arise. Of these six molecules, none have been reported experimen-tally, and calculated results have been reported in the literatureonly for the di(nitroso)oxalate, 4 [6].

On the other hand, when n = 1 or higher, because of the inabilityof the molecules to form carbon–carbon double or triple bonds ormaintain bonding to the ‘‘NO3’’ substituent without the addition ofhydrogen atoms or other substituents, only two alkane-derivativeisomers are expected to be observed: the nitritocarbonyl analogsof di(nitroso)oxalate and the nitratoxycarbon systems (ignoring‘‘mixed’’ isomers containing both the nitritocarbonyl and thenitratoxycarbon substituents for the sake of simplicity and compu-tational time and resources). These isomers are illustrated in Fig. 3for n = 1 (6 and 7) and in Fig. 4 for n = 2 (8 and 9). If mixed isomer

2210-271X/$ - see front matter ! 2011 Elsevier B.V. All rights reserved.doi:10.1016/j.comptc.2011.10.011

⇑ Corresponding author. Tel.: +1 707 826 3244; fax: +1 707 826 3279.E-mail address: rwz7001@humboldt.edu (R.W. Zoellner).

Computational and Theoretical Chemistry 979 (2012) 33–37

Contents lists available at SciVerse ScienceDirect

Computational and Theoretical Chemistry

journal homepage: www.elsevier .com/locate /comptc

Masaru  Kawakami.  Review  of  Scien,fic  Instruments,  83  (2012),  084303  

HapOc  Forces  

Atomic  Coordinates  

HapOc  PosiOon  

Feedback  Force  

3D  Ren

derin

g  

Caffeine  @  STO-­‐3G  

0  

0.02  

0.04  

0.06  

0.08  

0.1  

0.12  

0.14  

0.16  

0.18  

0.2  

0  

0.2  

0.4  

0.6  

0.8  

1  

1.2  

1   2   3   4   5   6   7   8  

1st  K

 Build  (secon

ds)  

Wall3me  (secon

ds)  

Number  of  GPUs  

38  S-­‐Shells  14  P-­‐Shells  

Total  SCF  

1st  K  Build  

Serial  Task  

ParallelUnit  

SSSS  

SSSS  

SSSS  

SSSP  

SSSP  

SSSP  

…  

…  

…  

Build_Exchange(…)  

MulO  GPU  Threading  

8  GTX  Titans  

2.069  ms  

1.464  ms  

1  GTX  Titan  

WaiOng  Tasks  

Completed  Tasks  

MulO  GPU  Streaming  

device()  

Stream()  

gpuAlloc(sz)  

cpuAlloc(sz)  

gpuFree(ptr)  

cpuFree(ptr)  (Pinned)  CPU  Buffer  

GPU  Buffer  

GpuCx   CX0  

CX1  

…  

CXN  

GPU  Pool  

GPU  Wrapper  Class  

GPU  Wrapper  Class  GpuCx* dev = GpuCx::CheckOut(); cudaStream_t strm = dev->stream(); double& hptr = dev->cpuAlloc(sz); ... double* dptr = dev->gpuAlloc(sz); cudaMemcpyAsync(dptr, hptr, sz, cudaMemcpyHostToDevice, strm); kern<<<gird, block, 0, strm>>>(dptr); ... GpuCx::Checkin(dev);

1  Titan  

7  Titans  

1  Titans  2  Streams  

Caffeine  @  STO-­‐3G  

38  S-­‐Shells  14  P-­‐Shells  0  

10  

20  

30  

40  

50  

0   1   2   3   4  

1st  Iter  K

 Build  (m

s)  

Physical  GPUs  

Caffeine  @  STO-­‐3G  

38  S-­‐Shells  14  P-­‐Shells  0  

0.2  

0.4  

0.6  

0.8  

1  

1.2  

1   2   3   4   5   6   7   8  

Wall3me  (secon

ds)  

Number  of  GPUs  

Before  

Aeer  

Molecule   Atoms   STO-­‐3G   6-­‐31G*  Imidazole   9   48  ms   287  ms  Caffeine   24   225  ms   1285  ms  Taxol   110   4297  ms   26.0  sec  

Caffeine   Taxol  

Imidazole  

Timings  for  full  SCF  +  Gradients  

Temp          300K  LnvTime    25fs  RHF/STO-­‐3G  TS  1.0fs  250ms  /  SCF  

RHF/6-­‐31G*  200ms  /  SCF  

RHF/STO-­‐3G  400ms  /  SCF  

RHF/6-­‐31G  200ms  /  SCF  

Conclusions  •  CUDA  is  a  powerful  framework  to  accelerate  scienOfic  programs  wriken  in  C.  

•  Using  GPUs,  interacOve  quantum  chemistry  is  possible  for  systems  up  to  a  few  dozen  atoms.  

•  Natural,  tacOle  computer  interfaces  provide  novel  applicaOons  for  computer  simulaOons.  

•  Responsive  models  provide  intuiOve  insight  for  discovery  and  educaOon.  

 

Acknowledgements  •  Prof.  Todd  MarOnez  •  Ivan  Ufimtsev  •  Alex  Jin