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 2022-4: Jaguar, Schrödinger, LLC, New York, NY, 2021.

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

"Quantitative structure-activity relationship(QSAR) models for color and COD removal for some dyes subjected to electrochemical oxidation"

Katha S. Hirpara, Upendra D. Patel, Environmental Technology, 2022, ,

"Aqueous redox flow battery using iron 2,2-bis(hydroxymethyl)-2,2′,2′-nitrilotriethanol complex and ferrocyanide as newly developed redox couple"

Mingyu Shin, Seunghye Oh, Hayoung Jeong, Chanho Noh, Yongjin Chung, Jeong Woo Han, Yongchai Kwon, Energy Research, 2022, 46(6), 8175-8185

· "Melt-state degradation mechanism of poly (ether ketone ketone): the role of branching on crystallization and rheological behavior"

Chris Croshaw, Levi Hamernik, Lina Ghanbari, Andrea Browning, Jeffrey Wiggins, Polymer Degradation and Stability, 2022, 200,

"The positional effect of arylamines on pyrene core in a blue fluorescent dopant significantly affecting the performance of organic light emitting diodes"

Yunho Ahn, Seonghyeon Kim, Jae Ho Song, Wonsik Yeom, Jihoon Lee, Min Chul Suh, Dyes and Pigments, 2022, 205, 110505

"Experimental Investigations of AlMg3 Components with Polyurethane and Graphene Oxide Nanosheets Composite Coatings, after Accelerated UV-Aging"

Alin Constantin Murariu, Lavinia Macarie, Luminita Crisan, and Nicoleta Pleşu, MDPI, 2022, 27(1),

"Thermal Grafting of Benzaldehyde for Preparing Catalytically Active Silicon Surface Evaluated by Electrical Methods"

R. Mallikarjun, Anum Mohammedi, Vaishnavi Kembhavi & Rajeev Joshi , Topics in Catalysis, 2022, ,

"Deep blue diboron embedded multi-resonance thermally activated delayed fluorescence emitters for narrowband organic light emitting diodes"

Kenkera Rayappa Naveen, Hyuna Lee, Ramanaskanda Braveenth, Ki Joon Yang, Soon Jae Hwang, Jang Hyuk Kwon, Chemical Engineering Journal, 2022, 432,

"Schiff base as n-type semiconductor: synthesis, characterization, and diode features"

Sneha Kagatikar, Dhanya Sunil & Dhananjaya Kekuda , Chemical Papers, 2022, ,

· "Transferable Neural Network Potential Energy Surfaces for Closed-Shell Organic Molecules: Extension to Ions"

Leif D. Jacobson, James M. Stevenson, Farhad Ramezanghorbani, Delaram Ghoreishi, Karl Leswing, Edward D. Harder, and Robert Abel, JCTC, 2022, 18(4), 2354-2366

"Understanding the Effect of Functionalization on Loading Capacity and Release of Drug from Mesoporous Silica Nanoparticles: A Computationally Driven Study"

Reema Narayan, Shivaprasad Gadag, Sanjay Garg, and Usha Y. Nayak, ACS Omega, 2022, 7(10), 8229-8245

"An easy to make Hg(II) complex as a selective and sensitive fluorescent turn-on chemosensor for iodide in an aqueous solution based on metal ion displacement mechanism"

K. Satheeshkumar, P. Saravana Kumar, R. Shanmugapriya, C. Nandhini, K.N. Vennila, Kuppanagounder P. Elango, Inorganic Chemistry Communications, 2022, 138,

"Comparative evaluation of ibuprofen co-crystals prepared by solvent evaporation and hot melt extrusion technology"

Sharvari M. Kshirsagar, Bandoo C. Chatale, Purnima D. Amin, JDDST, 2022, 67,

"Design of Molecules with Low Hole and Electron Reorganization Energy Using DFT Calculations and Bayesian Optimization"

Tatsuhito Ando, Naoto Shimizu, Norihisa Yamamoto, Nobuyuki N. Matsuzawa, Hiroyuki Maeshima, and Hiromasa Kaneko, The Journal of Physical Chemistry A, 2022, 126(36), 6336-6347

"Isolation of phytochemicals from Dolichandrone atrovirens followed by semisynthetic modification of ixoside via azomethine ylide cycloaddition; computational approach towards chemo-selection"

Meenakshi Singh, Bhakti Umesh Hirlekar, Shagufta Mondal, Suyash Pant, Devendra K. Dhaked, V. Ravichandiran, Abhijit Hazra & Yogesh P. Bharitkar, Natural Product Research, 2022, ,

"Revisiting Solvent-Dependent Roles of the Electrolyte Counteranion in Li–O2 Batteries upon CO2 Incorporation"

Filipe Marques Mota, Yeonseo Kim, Haeji Hong, Subin Yu, Sangheon Lee, and Dong Ha Kim, ACS Applied Energy Materials, 2022, 5(2), 2150-2160

"Effect of substituents on the crystal structure and thermal stability of N-phosphorylated iminophosphoranes"

Lilia Croitor, Mihaela Petric, Luminita Crisan, Paulina N. Bourosh, Gabriela Vlase, Titus Vlase & Manuela Crisan , Journal of Thermal Analysis and Calorimetry, 2022, 147, 5423-5435

"Organic electroluminescent device"

SOLUS ADVANCED MATERIALS CO., LTD, US20220006021A1, 2022, ,

"Intramolecular hydroxyl nucleophilic attack pathway by a polymeric water oxidation catalyst with single cobalt sites"

Hao Yang, Fusheng Li, Shaoqi Zhan, Yawen Liu, Wenlong Li, Qijun Meng, Alexander Kravchenko, Tianqi Liu, Yi Yang, Yuan Fang, Linqin Wang, Jiaqi Guan, István Furó, Mårten S. G. Ahlquist & Licheng Sun, Nature Catalysis, 2022, 5, 414-429

"Boronic Acid-Based n-Type Semiconductor for Electronic Device Application"

Sneha Kagatikar, Dhanya Sunil, Dhananjaya Kekuda, M. N. Satyanarayana, Suresh D. Kulkarni & Chaya Karkera , Journal of Electronic Materials, 2022, ,

"Carbene–Metal Complexes As Molecular Scaffolds for Construction of through-Space Thermally Activated Delayed Fluorescence Emitters"

Armands Ruduss, Baiba Turovska, Sergey Belyakov, Kitija A. Stucere, Aivars Vembris, and Kaspars Traskovskis, Inorg Chem, 2022, 61(4), 2174-2185

"Synthesis of indenocarbazole-based efficient deep-blue fluorescent emitter with a narrow emission band"

Eun Young Park, Seongjun Shin, Vasudevan Thangaraji, Soyeon Kim, Jihoon Lee, Min Chul Suh, Journal of Industrial and Engineering Chemistry, 2022, 107, 313-319

"Exploring the Mechanism of Cr(VI) Catalyzed Hypochlorous Acid Decomposition"

Michael Busch, Nina Simic, Elisabet Ahlberg, Chemistry Europe, 2022, ,

"Phenylpyridine and carbazole based host materials for highly efficient blue TADF OLEDs"

Tae Hoon Ha, Jong-Kwan Bin, Chil Won Lee, Organic Electronics, 2022, 102,

"Influence of side-chain length on antifungal efficacy of N-alkyl nicotinamide-based compounds"

Aleksandar Tot, Karolina Vrandečić, Jasenka Ćosić, Magdalena Matić, Milan Vraneš , Environmental Science and Pollution Research, 2022, ,

"Data-driven discovery of small electroactive molecules for energy storage in aqueous redox flow batteries"

Qi Zhang, Abhishek Khetan, Elif Sorkun, Fang Niu, Andrea Loss, Ilaria Pucher, Süleyman Er, Energy Storage Materials, 2022, 47, 167-177

· "De Novo Design of Molecules with Low Hole Reorganization Energy Based on a Quarter-Million Molecule DFT Screen: Part 2"

Joshua Staker, Kyle Marshall, Karl Leswing, Tim Robertson, Mathew D. Halls, Alexander Goldberg, Tsuguo Morisato, Hiroyuki Maeshima, Tatsuhito Ando, Hideyuki Arai, Masaru Sasago, Eiji Fujii, and Nobuyuki N. Matsuzawa, The Journal of Physical Chemistry A, 2022, 126(34), 5837-5852

"Enhancement of NO2 gas sensing ability through strong binding energy by modification of interface characteristics"

Yea Eun Hahm, Byung Ho Park, So Young Park, Tae Kyu An, Jihoon Lee, Yeong Don Park, Organic Electronics, 2022, 104,

"Qualitative and quantitative contributions of intermolecular interactions of dinuclear Ag complexes of sulfathiazole and sulfadiazine: X-ray crystallographic, Hirshfeld surface analysis, DFT studies and biological activities"

Mohammed Dawood Alalawy, Bhavesh N. Socha, Urmila H. Patel, R.H. Patel, Bhupesh S. Bhatt, Milan P. Dhaduk, Journal of Molecular Structure, 2022, 1255,

"Borane-catalyzed dehydrogenative C–C bond formation of indoles with N-tosylhydrazones: an experimental and computational study"

Dipika, Yogesh Brijwashi Sharma, Suyash Pant, Devendra Kumar Dhaked and Murali Mohan Guru , Organic Chemistry Frontiers, 2022, ,

"Olefin Metathesis Catalyzed by a Hoveyda–Grubbs-like Complex Chelated to Bis(2-mercaptoimidazolyl) Methane: A Predictive DFT Study"

J. Pablo Martínez and Bartosz Trzaskowski, Journal of Physical Chemistry A, 2022, 126(5), 720-732

· "Organic radical emitters: nature of doublet excitons in emissive layers"

Hadi Abroshan, Paul Winget, H. Shaun Kwak, Christopher T. Brown and Mathew D. Halls , Physical Chemistry Chemical Physics, 2022, 24, 16891-16899

· "Atomic Layer Deposition of Localized Boron- and Hydrogen-Doped Aluminum Oxide Using Trimethyl Borate as a Dopant Precursor"

Mattelaer, F.; Van Daele, M.; Minjauw, M.M.; Nisula, M.; Elliott, S.D.; Sajavaara, T.; Dendooven, J.; Detavernier, C., Chem. Mater., 2020, 32 (10), 4152–4165

· "Generation of Tautomers Using Micro-pKa’s"

Watson, M.A.; Yu, H.S.; Bochevarov, A.D., J. Chem. Inf. Model., 2019, 59(6), 2672-2689

"Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library"

Williams, T.N., Van Den Driessche, G.A., Valery, A.R.B., Fourches, D., Freeman, H.S., ACS Sustainable Chem. Eng., 2018, DOI: 10.1021/acssuschemeng.8b02882,

"Rapid assessment of conformational preferences in biaryl and aryl carbonyl fragments"

Sanfeliciano, S.M.G.; Schaus, JM, PLOS ONE, 2018, 13 (3), e0192974

· "Weighted Averaging Scheme and Local Atomic Descriptor for pKa Prediction Based on Density Functional Theory"

Yu, H., Watson, M., Bochevarov, A., J. Chem. Inf. Model., 2018, 58 (2), 271–286

· "Empirical Conversion of pKa Values between Different Solvents and Interpretation of the Parameters: Application to Water, Acetonitrile, Dimethyl Sulfoxide, and Methanol"

Rossini, E., Bochevarov, A., Knapp, E., ACS Omega, 2018, 3 (2), 1653–1662

· "Quantum chemical pKa prediction for complex organic molecules"

Philipp, D., Watson, M., Yu, H., Steinbrecher, T., Bochevarov, A. , Int. J. Quantum Chem, 2018, DOI: 10.1002/qua.25561, preprint

· "Automated Transition State Search and Its Application to Diverse Types of Organic Reactions"

Jacobson, L., Bochevarov, A., Watson, M., Hughes, T., Rinado, D., Ehrlich, S., Steinbrecher, T., Vaitheeswaran, S., Philipp, D., Halls, M., Friesner, R., J. Chem. Theory Comput., 2017, 13 (11), 5780–5797

· "Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules"

Cao, Y.; Hughes, T.; Giesen, D.; Halls, M.D.; Goldberg, A.; Vadicherla. T.A.; Sastry, M.; Patel, B.; Sherman, W.; Weisman, A.L.; Friesner, R.A., J Comput Chem., 2016, 37, 1425-1441

· "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

· "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

· "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

· "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

· "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

"Oxygen-evolving Mn cluster in photosystem II: The protonation pattern and oxidation state in the high-resolution crystal structure"

Galstyan, A.; Robertazzi, A.; Knapp, E.W., J. Am. Chem. Soc., 2012, 134, 7442–7449

· "A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: Parameterization against experimental and CCSD(T)-F12 heats of formation"

Hughes, T. F.; Harvey, J. N.; Friesner, R. A., Phys. Chem. Chem. Phys., 2012, 14, 7724-7738

"Mechanism of H2O2 decomposition on transition metal oxide surfaces"

Lousada, M.C.; Johansson, A.J.; Brinck, T.; Jonsson, M., J. Phys. Chem. C., 2012, 116, 9533–9543

"Electron-poor rhenium allenylidenes and their reactivity toward phosphines: A combined experimental and theoretical study"

Coletti, C.; Gonsalvi, L.; Guerriero, A.; Marvelli, L.; Peruzzini, M.; Reginato, G.; Re, N., Organometallics, 2012, 31(1), 57–69

"(rac)-1,1'-binaphthyl-based simple receptors designed for fluorometric discrimination of maleic and fumaric acids"

Ghosh, K.; Sen, T., J. Phys. Chem. B, 2011, 115, 8597-608

"Predicting Solvent Stability in Aprotic Electrolyte –Air Batteries: Nucleophilic Substitution by the Superoxide Anion Radical (O2•–)"

Bryantsev, V.S.; Giordani, V.; Walker, W.; Blanco, M.; Zecevic, S.; Sasaki, K.; Uddin, J.; Addison, D.; Chase, G.V., J. Phys. Chem. A, 2011, 115, 12399–12409

"Remarkable Stereospecific Conjugate Additions to the Hsp90 Inhibitor Celastrol"

Klaić, L.; Trippier, P.C.; Mishra R. K.; Morimoto, R.I.; Silverman, R.B., J. Am. Chem. Soc., 2011, 133, 19634–19637

"Charge Delocalization and Enhanced Acidity in Tricationic Superelectrophiles"

Naredla, R. R.; Zheng, C.; Nilsson Lill, S.O.; Klumpp, D. A., J. Am. Chem. Soc., 2011, 133, 13169–13175

· "Systematic investigation of the catalytic cycle of a single site ruthenium oxygen evolving complex using density functional theory"

Hughes, T.F.; Friesner, R.A., J. Phys. Chem. B, 2011, 115, 9280-9

"Mechanism for Degradation of Nafion in PEM Fuel Cells from Quantum Mechanics Calculations"

Yu, T. H.; Sha, Y.; Liu, W.-G.; Merinov, B.V.; Shirvanian, P.; Goddard, W.A., J. Am. Chem. Soc., 2011, 133, 19857–19863

"DFT Study on the Catalytic Reactivity of a Functional Model Complex for Intradiol-Cleaving Dioxygenases"

Georgiev, V.; Noack, H.; Borowski, T.; Blomberg, M.R.A.; Siegbahn, P.E.M., J. Phys. Chem. B, 2010, 114, 5878–5885

"Characterization of Proton Coupled Electron Transfer in a Biomimetic Oxomanganese Complex: Evaluation of the DFT B3LYP Level of Theory"

Wang, T.; Brudvig, G.; Batista, V. S., J. Chem. Theory Comput., 2010, 6, 755–760

"Elucidating the Ionomer-Electrified Metal Interface"

Kendrick, I.; Kumari, D.; Yakaboski, A.; Dimakis, D.; Smotkin, E.S., J. Am. Chem. Soc., 2010, 132, 17611–17616

"Unexpected Cleavage of 2-Azido-2-(hydroxymethyl)oxetanes: Conformation Determines Reaction Pathway? "

Farber, E.; Herget, J.; Gascón, J. A.; Howell, A.R., J. Org. Chem., 2010, 75, 7565–7572

· "Prediction of 57 Fe Mössbauer Parameters by Density Functional Theory: A Benchmark Study"

Bochevarov, A.D.; Friesner, R.A.; Lippard, S.J., J. Chem. Theory Comput., 2010, 6, 3735–3749

"Conformationally Restricted Homotryptamines. Part 7: 3-cis-(3-Aminocyclopentyl)indoles As Potent Selective Serotonin Reuptake Inhibitors"

King, H. D.; Meng, Z.; Deskus, J. A.; Sloan, C. P., Gao, Q.; Beno B.R.; Kozlowski, E.S.; LaPaglia, M.A.; Mattson, G.K.; Molski, T.F.; Taber, M.T.; Lodge, N.J.; Mattson, R.J.; Macor J.E., J. Med. Chem., 2010, 53, 7564–7572

"Modeling of isotope effects on binding oxamate to lactic dehydrogenase"

Swiderek K., Panczakiewicz A., Bujacz A., Bujacz G., Paneth P., J. Phys. Chem. B, 2009, 113, 12782-12789

· "Computational modeling of the electronic structure of Oligothiophenes with various side chains"

Wang T., Friesner R.A., J. Phys. Chem. C, 2009, 113, 2553-2561

"Understanding Rubredoxin Redox Potentials: Role of H-Bonds on Model Complexes"

Gámiz-Hernández, A. P.; Galstyan, A. S.; Knapp, E., J. Chem. Theory Comput., 2009, 5, 2898-2908

· "QM/MM simulation on P450 BM3 enzyme catalysis mechanism"

Tian L., Friesner R.A., J. Chem. Theory Comput., 2009, 5, 1421-1431

· "Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations"

Schneebeli S.T., Hall M.L., Breslow R., Friesner R., J. Am. Chem. Soc., 2009, 131, 3965-3973

"Peroxide-dependent formation of a covalent link between Trp51 and the heme in cytochrome c peroxidase"

Pipirou Z., Guallar V., Basran J., Metcalfe C.L., Murphy E.J., Bottrill A.R., Mistry S.C., Raven E.L., Biochemistry, 2009, 48, 3593-3599

· "Bonded Exciplex Formation: Electronic and Stereoelectronic Effects"

Wang, Y.; Haze, O.; Dinnocenzo, J. P.; Farid, S.; Farid, R. S.; Gould, I. R., J. Phys. Chem. A, 2008, 112, 13088–13094

· "Pseudospectral Time-Dependent Density Functional Theory"

Ko, C.; Malick, D.K.; Braden, D.A.; Friesner, R.A.; Martínez, T.J., J. Chem. Phys., 2008, 128, 104103-104111

"Heptahexaenylidene Complexes: Synthesis and Characterization of the First Complexes with an M=C=C=C=C=C=C=CR2 Moiety (M = Cr, W)"

Dede, M.; Drexler, M.; Fischer, H., Organometallics, 2007, 26, 4294-4299

"The inner-sphere process in the enantioselective Tsuji allylation reaction with (S)-t-Bu-phosphinooxazoline ligands"

Keith, J.; Behenna, D.C.; Mohr, J.T.; Ma, S.; Marinescu, S.C.; Oxgaard, J.; Stoltz, B.M., Goddard, W.A., J. Am. Chem. Soc., 2007, 129, 11876-11877

"Redox-Modulated Recognition of Tetrazines Using Thioureas"

Jordan, B. J.; Pollier, M. A.; Miller, L. A.; Tiernan, C.; Clavier, G.; Audebert, P.; Rotello, V.M., Org. Lett., 2007, 9, 2835–2838

"Torsion angle preference and energetics of small-molecule ligands bound to proteins"

Hao, M.; Haq, O.; Muegge, I., J. Chem. Inf. Model, 2007, 47, 2242-2252

"Synthesis and conformational analysis of novel trimeric maleimide cross-linking reagents"

Szczepanska, A.; Espartero, J.L.; Moreno-Vargas, A.J.; Carmona, A.T.; and Robina, I.; Remmert, S.; and Parish, C., J. Org. Chem., 2007, 72, 6776-6785

"Single-Molecule Junction Conductance through Diaminoacenes"

Quinn, J.; Foss, F.; Venkataraman, L.; Hybertsen, M.; Breslow, R., J. Am. Chem. Soc., 2007, 129, 6714-6715

"2,6-Disubstituted N-Arylsulfonyl Piperidines as Gamma-Secretase Inhibitors"

Pissarnitski, D.A.; Asberom, T.; Bara, T.A.; Buevich, A.V.; Clader, J.W.; Greenlee, W.J.; Guzik, H.S.; Josien, H.B.; Li, W.; McEwan, M.; McKittrick, B.A.; Nechuta, T.L.; Parker, E.M.; Sinning, L.; Smith, E.M.; Song, L.; Vaccaro, H.A.; Voigt, J.H.; Zhang, , Bioorganic & Medicinal Chemistry Letters, 2007, 17, 57-62

"Single-Site Vanadyl Activation, Functionalization, and Reoxidation Reaction Mechanism for Propane Oxidative Dehydrogenation on the Cubic V4O10 Cluster"

Cheng, M.; Chenoweth, K.; Oxgaard, J.; vanDuin, A.; Goddard, W., J. Phys. Chem. C, 2007, 111, 5115-5127

"Theoretical and Spectroscopic Study of Nickel(II) Porphyrin Derivatives"

Berrios, C.; Cardenas-Jiron, G.; Marco, J.; Gutierrez, C.; Ureta-Zanartu, M., J. Phys. Chem. A, 2007, 111, 2706-2714

· "Bonded Exciplexes. A New Concept in Photochemical Reactions"

Wang, Y.; Haze, O.; Dinnocenzo, J.P.; Farid, S.; Farid, R.S.; Gould, I.R., J. Org. Chem., 2007, 72, 6970-6981

"Electronics and Chemistry: Varying Single-Molecule Junction Conductance Using Chemical Substituents"

Venkataraman, L.; Park, Y.; Whalley, A.; Nuckolls, C.; Hybertsen, M.; Steigerwald, M., Nano Letters, 2007, 7, 502-506

"Unprecedented Formation of Azulenylidene Ligands by Reaction of the Vinylidene Ligand in Arylvinylidene Pentacarbonyl Complexes of Chromium and Tungsten with Alkoxyacetylenes"

Hagmayer, S.; Früh, A.; Haas, T.; Drexler, M.; Fischer, H., Organometallics, 2007, 26, 3791-3801

"Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case"

Blomberg, M.R.A.; Siegbahn, P.E.M., J. Comput. Chem. , 2006, 27, 1373-1384

"Hydroxide instead of bicarbonate in the structure of the oxygen evolving complex"

Siegbahn, P.E.M.; Lundberg, M., J. Inorg. Biochem. , 2006, 100, 1035-1040

· "Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from Ab Initio Quantum Chemistry"

Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A., J. Phys. Chem. A, 2004, 108, 621–627

· "Electronic Structure of Tubular Aromatic Molecules derived from the Metallic (5,5) Armchair Single Wall Carbon Nanotube"

Zhou, Z.; Steigerwald, M.; Hybertsen, M.; Brus, L.; Friesner, R. A., J. Am. Chem. Soc., 2004, 126, 3597–3607

· "Reversible surface oxidation and efficient luminescence quenching in semiconductor single-wall carbon nanotubes"

Dukovic, G.; White, B. E.; Zhou, Z. Y.; Wang, F.; Jockusch, S.; Steigerwald, M. L.; Heinz, T. F.; Friesner, R. A.; Turro, N. J.; Brus, L. E., J. Am. Chem. Soc., 2004, 126, 15269–15276

· "Scanning tunneling microscopy and theoretical study of competitive reactions in the dissociative chemisorption of CCl4 on iron oxide surfaces"

Rim, K.T.; Muller,T.; Fitts, J.P.; Adib, K.; Camillone, N.; Osgood, R.M.; Batista, E. R.; Friesner, R. A. ; Joyce, S. A.; Flynn, G. W., J. Phys. Chem. B., 2004, 108, 16753–16760

"DFT study of 1-D Li6Gd(BO3)(3)"

Rivas-Silva, J.F.; Flores-Riveros, A.; Berrondo, M., Int. J. Quantum Chem., 2003, 94, 105–112

· "Electronic Structure of 1 to 2 nm Diameter Silicon Core/Shell Nanocrystals: Surface Chemistry, Optical Spectra, Charge Transfer and Doping"

Zhou, Z.; Friesner, R. A.; Brus, L., J. Am. Chem. Soc., 2003, 125, 15599–15607

· "Action of HCl on 3-hydroxypyrazolo(iso)quinolines to give 1-chloropyrazoles: evidence for an addition-elimination mechanism by ab initio calculations in gas phase and water"

Greenwood, J. R.; Begtrup, M., Theor. Chem. Acc., 2003, 109, 200–205

· "Electronic Structure and Luminescence of 1.1-and 1.4-nm Silicon Nanocrystals: Oxide Shell versus Hydrogen Passivation"

Zhou, Z.; Brus, L.; Friesner, R. A., Nano Letters, 2003, 3, 163–167

· "Kinetics and Thermodynamics of H• Transfer From (h5-C5R5)Cr(CO)3H to Methyl Methacrylate and Styrene"

Tang, L.; Papish, E. T.; Abramo, G. P.; Norton, J. R.; Baik, M.; Friesner, R. A.; Rappé, A., J. Am. Chem. Soc., 2003, 125, 10093–10102

· "cis-{Pt(NH3)2(L)}2+/+ (L = Cl, H2O, NH3) Binding to Purines and CO: Does p-Back-Donation Play a Role?"

Baik, M.; Friesner, R. A.; Lippard, S. J., Inorg. Chem., 2003, 42, 8615–8617

· "A Computationally Inexpensive Modification of the Point Dipole Electrostatic Polarization Model for Molecular Simulations"

Kaminski, G. A.; Friesner, R. A.; Zhou, R., J. Comput. Chem., 2003, 24, 267–276

· "Computational Modeling for Scanning Tunneling Microscopy of Physisorbed Molecules via Ab Initio Quantum Chemistry"

Crystal, J.; Zhang, L. Y.; Friesner, R. A.; Flynn, G., J. Phys. Chem. A, 2002, 106, 1802–1814

· "Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase"

Guallar, V.; Gherman, B. F.; Miller, W. H.; Lippard, S. J.; Friesner, R.A., J. Am. Chem. Soc., 2002, 124, 3377–3384

· "Development of a Polarizable Force Field for Proteins via ab initio Quantum Chemistry: First Generation Model and Gas Phase Tests"

Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A.; Cao, Y. X.; Murphy, R. B.; Zhou, R.; Halgren, T. A., J. Comput. Chem., 2002, 23, 1515–1531

· "Computing Redox Potentials in Solution: Density Functional Theory as a Tool for Rational Design of Redox Agents"

Baik, M. H.; Friesner, R. A., J. Phys. Chem. A, 2002, 106, 7407–7412

· "A Non-Classical Hydrogen Bond in the Molybdenum Arene Complex [η6-C6H5C6H3(Ph)OH]Mo(PMe3)3: Evidence That Hydrogen Bonding Facilitates Oxidative Addition of the O–H Bond"

Tony, H.; Baik, M.; Bridgewater, B. M.; Shin, J. H.; Churchill, D. G.; Friesner, R. A.; Parkin, G. F., Chemical Communications, (British Royal Society), 2002, 22, 2644–2645

· "Accurate Prediction of Acidity Constants in Aqueous Solution via Density Functional Theory and Self-Consistent Reaction Field Methods"

Klicic, J. J. ; Friesner, R. A.; Liu, S. Y.; Guida, W. C., J. Phys. Chem. A, 2002, 106, 1327–1335

· "Ab Initio Quantum Calculation of the Diabatic Coupling Matrix Elemetns for the Self-Exchange Redox Couples M(Cp)2 0/+(M=Fe, Co; Cp=C5H5)"

Baik, M.; Crystal, J. B.; Friesner, R. A., Inorg. Chem., 2002, 41, 5926–5927

"Femtosecond Infrared Study of the Dynamics of Solvation and Solvent Caging"

Yang, H.; Snee, P. T.; Kotz, K. T.; Payne, C. K.; Harris, C. B., J. Am. Chem. Soc., 2001, 123, 4204

· "Large Scale Ab Initio Quantum Chemical Calculations on Biological Systems"

Friesner, R. A.; Dunietz, B. D., Accounts of Chemical Research, 2001, 34, 351–358

· "Activation of the C-H bond of Methane by Intermediate Q of Methane Monoozygenase: A Theoretical Study"

Gherman, B. F.; Dunietz, B. D.; Whittington, D. A.; Lippard, S. J.; Friesner, R. A., J. Am. Chem. Soc., 2001, 123, 3836–3837

"Protonation states of the chromophore of denatured green fluorescent proteins predicted by ab initio calculations"

El Yazal, J.; Prendergast, F.G.; Shaw, D. E.; Pang, Y. P., J. Am. Chem. Soc., 2000, 122, 11411–11415

Detailed Features

 

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 scripts
  • 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
  • GGA functionals: SOGGA, SOGGA11, HCTH407, GAM, N12, BOP, GLYP, KT2, rPBE, revPBE
  • Meta-GGA functionals: TPSS, revTPSS, SCAN, PKZB, MGGA-MS0, MGGA-MS1, MGGA-MS2
  • 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, B3LYP-LOC, M08-HX, M08-SO, MN12-L, MN15-L, and MN15, 
    ωB97X-D3, ωB97X-D3(BJ), ωB97X-V, ωB97M-V, TPSSh, revTPSSh, SOGGA11-X, SCAN0, MGGA-MS2h, MN12-SX
  • 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, CAM-B3LYP-D3, ωPBE-D3, B3LYP-D3(BJ),
    B3PW91-D3(BJ), PW6B95-D3(BJ), PBE0-D3(BJ), B1B95-D3(BJ), BP86-D3(BJ), BLYP-D3(BJ),
    OLYP-D3(BJ), PBE-D3(BJ), B97-D3(BJ), CAM-B3LYP-D3(BJ), ωPBE-D3(BJ), ωB97X-D3, ωB97X-D3(BJ)
  • Long range-corrected functionals: CAM-B3LYP, LRC-BLYP, uPBE, uPBE0, ωPBE, ωPBEh, HSE03, HSE06,
    M11, M11-L, ωB97, ωB97x, BNL, CAM-B3LYP-D3, ωPBE-D3, ωPBE-D3(BJ), ωB97X-D3, ωB97X-D3(BJ),
    MN12-SX, ωB97X-V, ωB97M-V
  • Dispersion-corrected long-range corrected functionals: CAM-B3LYP-D3, ωPBE-D3, ωB97X-D
  • 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, 6-31G, 6-311G(3df, 3pd), 6-31G(TM), D95, D95V,
    MSV, cc-pV[D,T,Q]Z, d-aug-cc-pv[D,T]Z, t-aug-cc-pv[D,T]Z, MIDIX, TZV, def2-svp, def2-svpd, def2-tzvp, def2-tzvpd, NLO-V, ANO-VT, PolX
  • Pseudospectral 3-21G, 6-31G, 6-311G, 6-31G(TM), D95, cc-pV[D,T,Q]Z, MIDIX, def2-svpd
  • Effective core potential (ECP) LAV1S, LAV2D, LAV2P, LAV3D, LAV3P, LACVD, LACVP,
    LACV3P, cc-pVTZ-pp, CSDZ, ERMLER2, LANL2DZ, LANL2TZ
  • 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 static polarizabilities, first and second hyperpolarizabilities 
  • Analytic dynamic (frequency-dependent) polarizabilities and hyperpolarizabilities
  • Fukui functions and atomic indices
  • Visualized noncovalent interactions
  • Natural bond orbital (NBO) analysis through the built-in third-party NBO 6.0 package
  • Harmonic and anharmonic 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 pKa prediction (available through a separate Jaguar pKa module)
  • Excited states through CIS and TDDFT theories

Spectroscopy:

  • Infrared (IR) intensities
  • Vibrational circular dichroism (VCD) spectra
  • Electronic circular dichroism (ECD) spectra
  • NMR shielding constants and chemical shifts in gas phase and solution
  • UV-vis spectra through CIS or TDDFT calculations
  • Visualizing IR, UV-vis, VCD, and ECD spectra through Maestro 
  • Automated alignment of theoretical and experimental VCD spectra in Maestro
  • Raman intensities 
  • Mössbauer isomer shifts and quadrupole splittings for 57Fe and other isotopes

Solvation:

  • Poisson-Boltzmann finite-element (PBF) self-consistent reaction field (SCRF),
    energies and geometry optimizations
  • van der Waals radii- and isodensity-based PBF
  • Several versions of polarizable continuum model (PCM), energies and geometry optimizations
  • SM6 and SM8 energies
  • Support for multiple solvents
  • Generation of COSMOTherm input files (.cosmo files)

Automated workflows:

  • Counterpoise calculations
  • pKa prediction (available through a separate Jaguar pKa module)
  • Intermolecular hydrogen bond binding energy
  • Fukui functions calculations
  • Heat of formation
  • VCD and ECD calculations
  • ΔE, ΔH, ΔG of a chemical reaction
  • Conformer and tautomer predictor

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
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