# Jaguar

Rapid ab initio electronic structure package

### The Advantages of *ab initio* Quantum Mechanics

Even with tremendous advances in molecular mechanical methods, there remain important research questions that cannot be answered without examining in detail a molecule's electronic structure. Also, molecular mechanics methods are limited by their parametrization. For example, conventional force fields either fail to treat metal containing systems, or experience large errors in computed results. High-level quantum mechanics is still the most accurate and most direct way to study these challenging systems, despite the increased computational cost.

An efficient quantum mechanical program is indispensable to the complete arsenal of any researcher who is interested in reactive chemistry, systems containing transition metals, or phenomena that require precise energetics.

**High performance:**

Jaguar proceeds much faster than conventional *ab initio* programs, making it possible to carry out many more calculations within the same time frame.

**Real-world systems:**

Jaguar scales well with molecular size, allowing it to be applied to larger, real-world problems without having to unrealistically reduce the size of the chemical system under study.

**Higher accuracy:**

Jaguar's performance advantage makes possible the application of higher levels of theory, resulting in more accurate energies and properties. Jaguar models important solvent effects by applying a self-consistent reaction field (SCRF).

**Chemical properties:**

Jaguar computes a comprehensive array of molecular properties including NMR, IR, UV-vis, VCD, pKa, partial charges, multipole moments, polarizabilities, molecular orbitals, electron density, electrostatic potential, Fukui functions, Mulliken population, and NBO analysis.

**Potential energy surface:**

Jaguar maps reaction coordinates between reactants, products, and transition states; Jaguar also generates potential energy surfaces with respect to variations in internal coordinates.

### Citations and Acknowledgements

**Schrödinger Release 2016-4**: Jaguar, Schrödinger, LLC, New York, NY, 2016.

**ö** Bochevarov, A.D.; Harder, E.; Hughes, T.F.; Greenwood, J.R.; Braden, D.A.; Philipp, D.M.; Rinaldo, D.; Halls, M.D.; Zhang, J.; Friesner, R.A., "Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences," Int. J. Quantum Chem., 2013, 113(18), 2110-2142

#### ö "Multiconformation, Density Functional Theory-Based pKa Prediction in Application to Large, Flexible Organic Molecules with Diverse Functional Groups"

Bochevarov, A. D.; Watson, M. A.; Greenwood, J. R.; Philipp, D. M., J. Chem. Theory Comput., 2016, 12 (12), 6001–6019#### ö "On the Rational Design of Zeolite Clusters"

Migues, A.N.; Muskat, A.; Auerbach, S.M.; Sherman, W.; Vaitheeswaran, S., ACS Catal., 2015, 5, 2859-2865#### ö "Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences"

Bochevarov, A.D.; Harder, E.; Hughes, T.F.; Greenwood, J.R.; Braden, D.A.; Philipp, D.M.; Rinaldo, D.; Halls, M.D.; Zhang, J.; Friesner, R.A., Int. J. Quantum Chem., 2013, 113(18), 2110-2142#### ö "Virtual screening of electron acceptor materials for organic photovoltaic applications"

Halls, M.D.; Djurovich, P.J.; Giesen, D.J.; Goldberg, A.; Sommer, J.; McAnally, E.; Thompson, M.E., New J. Phys., 2013, 15, 105029#### ö "Close intramolecular sulfur–oxygen contacts: Modified force field parameters for improved conformation generation"

Lupyan, D.; Abramov, Y.A.; Sherman, W., J. Comput. Aided Mol. Des., 2012, 26, 1195-1205#### Detailed Features in Release 2016-4

**General: **

- Graphical interface and interaction with other Schrödinger software through Maestro
- Optional pseudospectral integrals greatly speed up calculations
- Key modules are parallelized
- High-quality initial guess for transition metals
- Automated workflows through Python scipts
- Designed for solving real-world problems involving large systems
- Sophisticated job control
- Runs on Linux, OS X, and Windows
- Fast and reliable technical support

**Methods:**

Density functional theory (DFT):

- Exchange functionals: HFS, Xalpha, Becke 88, PW91, Barone-modified PW91, OPTX
- Correlation functionals: VWN, VWN5, LYP, P86, PW91, B95, Perdew-Zunger 81, PBE, HCTH407
- Hybrid functionals: B3LYP, O3LYP, X3LYP, B3P86, B3PW91, B97-1, B98, SB98, PBE0, PWB6K,

PW6B95, MPW1K, MPWB1K, MPW1PW91, BB1K, BHandH, BHandHLYP, M05, M05-2X, M06,

M06-2X, M06-L, M06-HF, PBE, HCTH407, B3LYP-LOC, M08-HX, and M08-SO - Dispersion-corrected functionals: B97-D, B3LYP-D3, B3PW91-D3, MPWB1K-D3, M05-D3,

M05-2X-D3, M06-D3, M06-HF-D3, M06-2X-D3, PBE0-D3, B1B95-D3, BP86-D3, BLYP-D3,

OLYP-D3, PBE-D3, B97-D3, B3LYP-MM, PBE-ulg - Long range-corrected functionals: CAM-B3LYP, LRC-BLYP, uPBE, uPBE0, ωPBE, ωPBEh, HSE03, HSE06, M11, M11-L, ωB97, ωB97x, BNL
- Dispersion-corrected long-range corrected functionals: CAM-B3LYP-D3 and ωPBE-D3
- Restricted (RHF), unrestricted (UHF), and spin-restricted (ROHF) wave functions
- Energies and gradients are available for all, and second derivatives for the vast majority of

the functionals (including D3-corrected)

Hartree-Fock (HF):

- RHF, UHF, and ROHF wave functions
- Energies, gradients, and second derivatives

Local Møller-Plesset perturbation theory (LMP2):

- RHF and ROHF wave functions
- Energies, gradients, and numerical second derivatives

Time-dependent density functional theory (TDDFT) and Configuration interaction singles (CIS):

- RHF wave functions
- Energies, gradients, and second derivatives

Zeroth Order Regular Approximation (ZORA):

- Energies
- Scalar and spin-orbit Hamiltonians
- Can be combined with TDDFT

**Basis sets:**

- Gaussian-type orbitals (GTO)
- s, p, d, f functions
- Analytic STO-3G, 3-21G, 4-21G, 4-31G, 6-21G, 6-311G(3df, 3pd), 6-31G(TM), D95, D95V,

MSV, cc-pV[D,T,Q]z, MIDIX, TZV, Rappoport-svpd - Pseudospectral 3-21G, 6-31G, 6-311G, 6-31G(TM), D95, cc-pV[D,T,Q]z, MIDIX, Rappoport-svpd
- Effective core potential (ECP) LAV1S, LAV2D, LAV2P, LAV3D, LAV3P, LACVD, LACVP,

LACV3P, cc-pVTZ-pp, CSDZ, ERMLER2 - Relativistic sarc-zora, dyall-v2z_zora-j-pt-gen, and dyall-2zcvp_zora-j-pt-gen
- Diffuse and/or polarization functions are available for most basis sets
- Custom basis set and automatic conversion from Gaussian to Jaguar format
- Automated counterpoise calculations

**Geometry Optimizations:**

- Geometry optimizations for equilibrium structures and transition states, in gas phase

and solution - Geometry optimizations of excited states with TDDFT
- Cartesian, redundant, and internal coordinates
- Constraints on bond lengths, bond angles, torsional angles
- Constraints on Cartesian or internal coordinates, frozen or harmonic
- Standard, linear synchronous transit (LST), and quadratic synchronous transit (QST)

transition state optimizations - Fischer-Almlöf, Schlegel, user-supplied, and quantum-mechanical Hessian guesses;

BFGS, Powell, and Murtagh-Sargent/Powell Hessian updates - Intrinsic reaction coordinate (IRC) scans
- Relaxed and rigid coordinate scans
- Post-convergence analysis
- Prevent chemical reactions during geometry optimizations

**Molecular Properties:**

- Electrostatic potential (ESP) surface and analysis
- Average local ionization energy (ALIE) surface
- Electron density and spin density surfaces
- Dipole, quadrupole, octupole, and hexadecapole moments
- Analytic polarizabilities, first and second hyperpolarizabilities
- Fukui functions and atomic indices
- Visualized noncovalent interactions
- Natural bond orbital (NBO) analysis through the built-in third-party NBO 6.0 package
- Vibrational frequencies
- Mulliken population analysis
- Mulliken, ESP, and Stockholder charges
- Thermochemical properties: constant volume heat capacity, internal energy, enthalpy,

entropy, Gibbs free energy at varying temperatures and pressures, heat of formation *Ab initio*pK_{a}prediction (available through a separate Jaguar pK_{a}module)- Excited states through CIS and TDDFT theories

**Spectroscopy:**

- Infrared (IR) intensities
- Vibrational circular dichroism (VCD) spectra
- NMR shielding constants and chemical shifts in gas phase and solution
- UV-vis spectra through CIS or TDDFT calculations
- Visualizing IR, UV-vis, and VCD spectra through Maestro
- Raman intensities

#### Solvation:

- Poisson-Boltzmann finite-element (PBF) self-consistent reaction field (SCRF),

energies and geometry optimizations - van der Waals radii- and isodensity-based PBF
- SM6 and SM8 energies
- Multiple solvents

**Automated workflows:**

- Counterpoise calculations
- pK
_{a}prediction (available through a separate Jaguar pK_{a}module) - Intermolecular hydrogen bond binding energy
- Fukui functions calculations
- Heat of formation
- VCD calculations
- ΔE, ΔH, ΔG of a chemical reaction

#### Parallel:

- Analytic and pseudospectral calculations
- HF and DFT energies
- HF and DFT geometry optimizations
- HF and DFT second derivatives (vibrational frequencies)
- HF and DFT VCD spectra
- Closed-shell LMP2 energies
- CIS and TDDFT energies
- NMR shielding constants
- Polarizabilities and hyperpolarizabilities
- SM6 and SM8 solvation models