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Science

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(Science with NWChem)
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=Science with NWChem=
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=NWChem Related Publications=
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NWChem used by thousands of researchers worldwide to investigate questions about chemical processes by applying theoretical techniques to predict the structure, properties, and reactivity of chemical and biological species ranging in size from tens to millions of atoms. With NWChem, researchers can tackle molecular systems including biomolecules, nanostructures, actinide complexes, and materials. NWChem offers an extensive array of highly scalable, parallel computational chemistry methods needed to address scientific questions that are relevant to reactive chemical processes occurring in our everyday environment—photosynthesis, protein functions, and combustion, to name a few.  They include a multitude of highly correlated methods, density functional theory (DFT) with an extensive set of exchange-correlation functionals, time-dependent density functional theory (TDDFT), plane-wave DFT with exact exchange and Car-Parrinello, molecular dynamics with AMBER and CHARMM force fields, and combinations of them.
 
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'''A list of research publications that utilized NWChem can be found [http://www.emsl.pnnl.gov/emslweb/nwchem-related-publications here]'''.
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NWChem-related publications are publications detected via a Web-based search that either acknowledge or use NWChem.
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=Ground State DFT Calculations=
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2016 publications
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The local basis implementation of DFT in NWChem uses Gaussian atom centered Gaussian type orbitals (GTO) and can be used to study molecular, finite clusters and nanosystems. An exhaustive list of exchange-correlation functionals are supported including: traditional DFT, hybrid functionals, meta-type functionals, range-separated forms, double-hybrid functionals and dispersion corrections. All the available exchange-correlation functionals have associated analytic first derivatives and most functionals have associated second derivatives. Relativistic effects can also be included in DFT/HF calculations via the all-electron spin-free and spin–orbit one-electron Douglas–Kroll–Hess (DKH) method and zeroth-order relativistic approximation (ZORA) as well as through effective core (ECP) and spin–orbit (SO) potentials.
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* Abburu S, V Venkatraman, and BK Alsberg. 2016. "TD-DFT Based Fine-Tuning of Molecular Excitation Energies Using Evolutionary Algorithms." RSC Advances 6:3661-3670.
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* Aprà E and K Kowalski. 2016. "Implementation of High-Order Multireference Coupled-Cluster Methods on Intel Many Integrated Core Architecture." Journal of Chemical Theory and Computation 12:1129-1138.
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* Aslan M, JBA Davis, and RL Johnston. 2016. "Global Optimization of Small Bimetallic Pd-Co Binary Nanoalloy Clusters: A Genetic Algorithm Approach at the DFT Level." Physical Chemistry Chemical Physics 18:6676-6682.
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* Brémond É, M Savarese, NQ Su, ÁJ Pérez-Jiménez, X Xu, JC Sancho-García, and C Adamo. 2016. "Benchmarking Density Functionals on Structural Parameters of Small-/Medium-Sized Organic Molecules." Journal of Chemical Theory and Computation 12:459-465.
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* Brown DML, H Cho, and WA de Jong. 2016. "Bridging Experiment and Theory: A Template for Unifying NMR Data and Electronic Structure Calculations." Journal of Cheminformatics Article no. 8.
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* Brůhová Michalčíková R, K Dryahina, and P Španěl. 2016. "SIFT-MS Quantification of Several Breath Biomarkers of Inflammatory Bowel Disease, IBD: A Detailed Study of the Ion Chemistry." International Journal of Mass Spectrometry 396:35-41.
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* Collins RN, KM Rosso, AL Rose, CJ Glover, and T David Waite. 2016. "An in situ XAS Study of Ferric Iron Hydrolysis and Precipitation in the Presence of Perchlorate, Nitrate, Chloride and Sulfate." Geochimica et Cosmochimica Acta 177:150-169.
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* Chow E, X Liu, S Misra, M Dukhan, M Smelyanskiy, JR Hammond, Y Du, X-K Liao, and P Dubey. 2016. "Scaling up Hartree-Fock Calculations on Tianhe-2." International Journal of High Performance Computing Applications 30:85-102.
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* Chwee TS, GS Lim, ZC Wong, MB Sullivan, and WY Fan. 2016. "Rapid Intersystem Crossings in Anti Bimanes." Physical Chemistry Chemical Physics 18:7404-7413.
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* Cochrane B and FY Naumkin. 2016. "Reshaping and Linking of Molecules in Ion-Pair Traps." Chemical Physics Letters 643:137-141.
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* Deb N, B Li, M Skoda, S Rogers, Y Sun, X Gong, A Karim, BG Sumpter, and DG Bucknall. 2016. "Harnessing Structure–Property Relationships for Poly(alkyl thiophene)–Fullerene Derivative Thin Films to Optimize Performance in Photovoltaic Devices." Advanced Functional Materials 26:1908-1920.
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* Fang Z, P Zetterholm, and DA Dixon. 2016. "1,2-Ethanediol and 1,3-Propanediol Conversions over (MO3)3 (M = Mo, W) Nanoclusters: A Computational Study." The Journal of Physical Chemistry A 120:1897-1907.
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* Fischer SA, TW Ueltschi, PZ El-Khoury, AL Mifflin, WP Hess, H-F Wang, CJ Cramer, and N Govind. 2016. "Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C–H Region of DMSO as a Case Study." The Journal of Physical Chemistry B 120:1429-1436.
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* Gálvez O, M Teresa Baeza-Romero, M Sanz, and LF Pacios. 2016. "A Theoretical Study on the Reaction of Ozone with Aqueous Iodide." Physical Chemistry Chemical Physics 18:7651-7660.
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* Gao M, AJ Misquitta, LHN Rimmer, and MT Dove. 2016. "Molecular Dynamics Simulation Study of Various Zeolitic Imidazolate Framework Structures." Dalton Transactions 45:4289-4302.
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* Ghuman KK, LB Hoch, P Szymanski, JYY Loh, NP Kherani, MA El-Sayed, GA Ozin, and CV Singh. 2016. "Photoexcited Surface Frustrated Lewis Pairs for Heterogeneous Photocatalytic CO2 Reduction." Journal of the American Chemical Society 138:1206-1214.
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* Grimmel S, G Schoendorff, and AK Wilson. 2016. "Gauging the Performance of Density Functionals for Lanthanide-Containing Molecules." Journal of Chemical Theory and Computation 12:1259-1266.
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* Haghdani S, P-O Åstrand, and H Koch. 2016. "Optical Rotation from Coupled Cluster and Density Functional Theory: The Role of Basis Set Convergence." Journal of Chemical Theory and Computation 12:535-548.
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* Hu H-S, Y-F Zhao, JR Hammond, EJ Bylaska, E Aprà, HJJ van Dam, J Li, N Govind, and K Kowalski. 2016. "Theoretical Studies of the Global Minima and Polarizabilities of Small Lithium Clusters." Chemical Physics Letters 644:235-242.
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* Huang W and J-L Liao. 2016. "Catalytic Mechanism of the Maltose Transporter Hydrolyzing ATP." Biochemistry 55:224-231.
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* Jacobs MJ, G Schneider, and KG Blank. 2016. "Mechanical Reversibility of Strain-Promoted Azide–Alkyne Cycloaddition Reactions." Angewandte Chemie International Edition 55:2899-2902.
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* Karadakov PB. 2016. "Do Large Polycyclic Aromatic Hydrocarbons and Graphene Bend? How Popular Theoretical Methods Complicate Finding the Answer to This Question." Chemical Physics Letters 646:190-196.
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* Khrenova MG, ED Kots, AM Kulakova, and IV Polyakov. 2016. "Modeling GTP Hydrolysis in RasGAP Protein Complex." Moscow University Chemistry Bulletin 71:21-24.
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* Kladnik G, M Puppin, M Coreno, M de Simone, L Floreano, A Verdini, A Morgante, D Cvetko, and A Cossaro. 2016. "Ultrafast Charge Transfer Pathways through a Prototype Amino-Carboxylic Molecular Junction." Nano Letters 16:1955-1959.
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* Köç M, Y Zorlu, U İşci, S Berber, V Ahsen, and F Dumoulin. 2016. "A Library of Dimeric and Trimeric Phthalonitriles Linked by a Single Aromatic Ring: Comparative Structural and DFT Investigations." CrystEngComm 18:1416-1426.
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* Kozlov MI, VV Poddubnyy, IO Glebov, AS Belov, and DV Khokhlov. 2016. "Ab initio Calculation of Excitonic Hamiltonian of Light-Harvesting Complex LH1 of Thermochromatium tepidum." Chemical Physics Letters 645:48-52.
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* Kuisma MJ, AM Lundin, K Moth-Poulsen, P Hyldgaard, and P Erhart. 2016. "Comparative Ab-Initio Study of Substituted Norbornadiene-Quadricyclane Compounds for Solar Thermal Storage." The Journal of Physical Chemistry C 120:3635-3645.
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* Kumar RP, L Roopa, U Nongthomba, MM Sudheer Mohammed, and N Kulkarni. 2016. "Docking, Molecular Dynamics and QM/MM Studies to Delineate the Mode of Binding of CucurbitacinE to F-actin." Journal of Molecular Graphics and Modelling 63:29-37.
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* Lv J, J Zhang, and D Wang. 2016. "A Multi-Level Quantum Mechanics and Molecular Mechanics Study of SN2 Reaction at Nitrogen: NH2Cl + OH- in Aqueous Solution." Physical Chemistry Chemical Physics 18:6146-6152.
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* Manaa MR, LE Fried, and I-FW Kuo. 2016. "Determination of Enthalpies of Formation of Energetic Molecules with Composite Quantum Chemical Methods." Chemical Physics Letters 648:31-35.
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* Mancuso R, DS Raut, N Marino, G De Luca, C Giordano, S Catalano, I Barone, S Andò, and B Gabriele. 2016. "A Palladium-Catalyzed Carbonylation Approach to Eight-Membered Lactam Derivatives with Antitumor Activity." Chemistry – A European Journal 22:3053-3064.
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* Mendoza-Huizar LH, G Salgado-Morán, R Ramirez-Tagle, and D Glossman-Mitnik. 2016. "A Theoretical Quantum Study of the Intramolecular Interactions and Chemical Reactivity of Polymorphs A and B of Famotidine in the Gas, DMSO, and Aqueous Phases." Computational and Theoretical Chemistry 1075:54-62.
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* Moore JE and L Jensen. 2016. "Orbital Renormalization Effects on the Coupling between Molecular Excitations and Plasmons." The Journal of Physical Chemistry C 120:5659-5666.
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* Mosquera MA, CH Borca, MA Ratner, and GC Schatz. 2016. "Connection between Hybrid Functionals and Importance of the Local Density Approximation." The Journal of Physical Chemistry A 120:1605-1612.
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* Nemukhin AV, AM Kulakova, SV Lushchekina, AY Ermilov, and SD Varfolomeev. 2016. "Modeling Chemical Transformations at the Active Sites of Cholinesterases by Quantum-Based Simulations." Moscow University Chemistry Bulletin 70:274-277.
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* Pérez-Soto R, SA Vázquez, and E Martínez-Núñez. 2016. "Photodissociation of Acryloyl Chloride at 193 nm: Interpretation of the Product Energy Distributions, and New Elimination Pathways." Physical Chemistry Chemical Physics 18:5019-5026.
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* Perlikowska R, J Piekielna, L Gentilucci, R De Marco, MC Cerlesi, G Calo, R Artali, C Tömböly, A Kluczyk, and A Janecka. 2016. "Synthesis of Mixed MOR/KOR Efficacy Cyclic Opioid Peptide Analogs with Antinociceptive Activity after Systemic Administration." European Journal of Medicinal Chemistry 109:276-286.
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* Petitjean L, R Gagne, ES Beach, D Xiao, and PT Anastas. 2016. "Highly Selective Hydrogenation and Hydrogenolysis Using a Copper-Doped Porous Metal Oxide Catalyst." Green Chemistry 18:150-156.
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* Rippy KC, EV Bukovsky, TT Clikeman, Y-S Chen, G-L Hou, X-B Wang, AA Popov, OV Boltalina, and SH Strauss. 2016. "Copper Causes Regiospecific Formation of C4F8-Containing Six-Membered Rings and Their Defluorination/Aromatization to C4F4-Containing Rings in Triphenylene/1,4-C4F8I2 Reactions." Chemistry – A European Journal 22:874-877.
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* Savoy ES and FA Escobedo. 2016. "Molecular Simulation of the Effects of Humidity and of Interfacial Si- and B-Hydroxyls on the Adhesion Energy between Glass Plates." Journal of Colloid and Interface Science 465:233-241.
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* Sergentu D-C, D Teze, A Sabatié-Gogova, C Alliot, N Guo, F Bassal, I Da Silva, D Deniaud, R Maurice, J Champion, N Galland, and G Montavon. 2016. "Advances on the Determination of the Astatine Pourbaix Diagram: Predomination of AtO(OH)2− over At− in Basic Conditions." Chemistry – A European Journal 22:2964-2971.
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* Singh G, AC Chamberlin, HR Zhekova, SY Noskov, and DP Tieleman. 2016. "Two-Dimensional Potentials of Mean Force of Nile Red in Intact and Damaged Model Bilayers. Application to Calculations of Fluorescence Spectra." Journal of Chemical Theory and Computation 12:364-371.
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* Soniat M, G Pool, L Franklin, and SW Rick. 2016. "Ion Association in Aqueous Solution." Fluid Phase Equilibria 407:31-38.
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* Soriano-Agueda LA, C Ortega-Moo, J Garza, JA Guevara-García, and R Vargas. 2016. "Formation of Reactive Oxygen Species by Vanadium Complexes." Computational and Theoretical Chemistry 1077:99-105.
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* Sun H, S Zhang, C Zhong, and Z Sun. 2016. "Theoretical Study of Excited States of DNA Base Dimers and Tetramers Using Optimally Tuned Range-Separated Density Functional Theory." Journal of Computational Chemistry 37:684-693.
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* Swenson NK, MA Ratner, and EA Weiss. 2016. "Computational Study of the Influence of the Binding Geometries of Organic Ligands on the Photoluminescence Quantum Yield of CdSe Clusters." The Journal of Physical Chemistry C 120:6859-6868.
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* Tainter CJ and GC Schatz. 2016. "Reactive Force Field Modeling of Zinc Oxide Nanoparticle Formation." The Journal of Physical Chemistry C 120:2950-2961.
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* Tan M-L, BS Perrin, S Niu, Q Huang, and T Ichiye. 2016. "Protein Dynamics and the All-Ferrous [Fe4S4] Cluster in the Nitrogenase Iron Protein." Protein Science 25:12-18.
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* Ueltschi TW, SA Fischer, E Aprà, AN Tarnovsky, N Govind, PZ El-Khoury, and WP Hess. 2016. "Time-Domain Simulations of Transient Species in Experimentally Relevant Environments." The Journal of Physical Chemistry A 120:556-561.
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* Valiev M, SHM Deng, and X-B Wang. 2016. "How Anion Chaotrope Changes the Local Structure of Water: Insights from Photoelectron Spectroscopy and Theoretical Modeling of SCN–  Water Clusters." The Journal of Physical Chemistry B 120:1518-1525.
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* Verma P, WD Derricotte, and FA Evangelista. 2016. "Predicting Near Edge X-ray Absorption Spectra with the Spin-Free Exact-Two-Component Hamiltonian and Orthogonality Constrained Density Functional Theory." Journal of Chemical Theory and Computation 12:144-156.
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* Wang J, L Liu, and AK Wilson. 2016. "Oxidative Cleavage of the β-O-4 Linkage of Lignin by Transition Metals: Catalytic Properties and the Performance of Density Functionals." The Journal of Physical Chemistry A 120:737-746.
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* Webre WA, JP Hill, Y Matsushita, PA Karr, K Ariga, and F D'Souza. 2016. "Anion Binding, Electrochemistry and Solvatochromism of β-Brominated Oxoporphyrinogens." Dalton Transactions 45:4006-4016.
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* Yao H, Q Dai, and Z You. 2016. "Molecular Dynamics Simulation of Physicochemical Properties of the Asphalt Model." Fuel 164:83-93.
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* Yoo K, AM Dive, S Kazemiabnavi, S Banerjee, and P Dutta. 2016. "Effects of Operating Temperature on the Electrical Performance of a Li-air Battery Operated with Ionic Liquid Electrolyte." Electrochimica Acta 194:317-329.
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* Zhang J, AL Weisman, P Saitta, and RA Friesner. 2016. "Efficient Simulation of Large Materials Clusters Using the Jaguar Quantum Chemistry Program: Parallelization and Wavefunction Initialization." International Journal of Quantum Chemistry 116:357-368.
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* Zhang J, L Yang, J Xie, and WL Hase. 2016. "Microsolvated F–(H2O) + CH3I SN2 Reaction Dynamics. Insight into the Suppressed Formation of Solvated Products." The Journal of Physical Chemistry Letters 7:660-665.
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* Zhang Y, DA Williams, SA Zaidi, Y Yuan, A Braithwaite, EJ Bilsky, WL Dewey, HI Akbarali, JM Streicher, and DE Selley. 2016. "17-Cyclopropylmethyl-3,14β-dihydroxy-4,5α-epoxy-6β-(4′-pyridylcarboxamido)morphinan (NAP) Modulating the Mu Opioid Receptor in a Biased Fashion." ACS Chemical Neuroscience 7:297-304.
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* Zheng L, NF Polizzi, AR Dave, A Migliore, and DN Beratan. 2016. "Where Is the Electronic Oscillator Strength? Mapping Oscillator Strength across Molecular Absorption Spectra." The Journal of Physical Chemistry A 120:1933-1943.
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<center><gallery widths=170px perrow=5>
 
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File:rochefort_2010.png|<small>''[http://www.rsc.org/delivery/_ArticleLinking/ArticleLinking.cfm?JournalCode=CC&Year=2010&ManuscriptID=b926286e&Iss=17 Adsorption of aminotriazines on graphene using dispersion corrected DFT]</small>
 
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File:amity_zeolite.png|<small>''Formyl cation bound to a Bronsted acid site in a zeolite cavity</small>
 
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File:tio2_160.png|<small>''[http://www.mrs.org/s_mrs/sec_subscribe.asp?CID=26171&DID=325813&action=detail Ground and excited state properties of TiO<sub>2</sub> rutile]</small>
 
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File:waters.png|<small>''[http://jcp.aip.org/resource/1/jcpsa6/v131/i21/p214103_s1 Dipole polarizabilities of water clusters]</small>
 
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File:sic_nano.png|<small>''Ground and excited state properties of SiC nanoclusters</small>
 
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</gallery></center>
 
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=Excited State Calculations with TDDFT=
 
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TDDFT has become an attractive and efficient tool for reliable excited-state calculations involving single excitations in a wide range of systems spanning molecules to materials. However, a major drawback lies in the quality of the exchange-correlation functionals. It is well known that various commonly used functionals are reasonably accurate for valence excited states but fall short in the prediction of charge-transfer (CT) and Rydberg states. The recently developed range-separated functionals have been shown to be very encouraging for CT transitions and outperform their non-range-separated counterparts. Results with these functionals are also comparable with very high levels of theory like EOMCC. In addition to an exhaustive list of commonly used exchange-correlation functionals, several range-separated forms have been recently implemented and extensively validated in NWChem.
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'''full list of research publications that utilized NWChem can be found [http://www.emsl.pnnl.gov/emslweb/nwchem-related-publications here]'''.
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<center><gallery widths=170px perrow=5>
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File:porphyrin_water.png|<small>''[http://pubs.acs.org/doi/full/10.1021/jp902118k Charge transfer excitations in Zinc Porphyrin in aqueous solution]</small>
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File:ATbasepair.png|<small>''[http://pubs.acs.org/doi/full/10.1021/jp905893v Correct lowest excitation in the AT base pair]</small>
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File:p2ta.png|<small>''[http://jcp.aip.org/jcpsa6/v132/i15/p154103_s1 Excitation energies for the oligoporphyrin dimer calculated with range-separated TDDFT are in very good agreement with EOMCC and experimental data]</small>
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File:chromophores.png|<small>''[http://pubs.acs.org/doi/abs/10.1021/ct900231r Optical spectra of TCF-Chromophores]</small>
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File:ag20.png|<small>''[http://jcp.aip.org/resource/1/jcpsa6/v132/i19/p194302_s1 Optical properties of silver clusters]</small>
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</gallery></center>
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=High Accuracy Is Scalable to Large Problem Sizes=
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A comprehensive understanding of excited-state processes is crucial in many areas of chemistry, and NWChem has the methodologies capable of providing reliable characterization of excitation energies and excited-state potential energies. Several recent implementations based on the Equation-of-Motion Coupled Cluster (EOMCC) formalism offer a unique chance to address these problems.  The largest up-to-date EOMCC calculations demonstrated that taking advantage of ever growing computer power the calculations with the EOMCC methodologies are possible for systems composed of 200-300 correlated electrons.
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<center><gallery widths=170px perrow=5>
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File:P2ta_ver1.png|<small>''[http://jcp.aip.org/jcpsa6/v132/i15/p154103_s1 The EOMCC excitation energies for the oligoporphyrin dimer  are in a very good agreement with experimentally inferred values]</small>
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File:All_trans_beta_carotene_final_dft_ccpvtz.png|<small>''New EOMCC formalisms can be used to study systems of biological relevance (&beta;-carotene)</small>
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File:Spiro.PNG|<small>''[http://pubs.acs.org/doi/abs/10.1021/jp101761d Highly correlated EOMCC methods accounting for higher-correlation effects can be used to describe electron transfer processes in challenging  open-shell systems]</small>
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File:Tio2_doped.png|<small>''[http://dx.doi.org/10.1016/j.cplett.2009.01.073 New EOMCC models for multiscale approaches  provide efficient tool for modeling excite states in true environment]</small>
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File:Tce_picture_new.png|<small>''Tensor Contraction Engine (TCE)  generated EOMCC codes can take advantage of massively parallel compute. The CR-EOMCCSD(T) implementation was shown to scale across 34,008 cores''</small>
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</gallery></center>
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NWChem offers several variants of the EOMCC formalism – from rudimentary EOMCC model with singles and doubles (EOMCCSD) to more sophisticated methods accounting for the effect of  triple excitations such as the non-iterative CR-EOMCCSD(T) method  and the iterative EOMCCSDT approach and its active-space variant. These accurate formalisms can be used not only for calculations of vertical excitation energies but also to characterize excited-state potential energy surfaces. Various EOMCC approaches can be fully integrated with the multiscale approaches enabling the simulations of the excited-state processes in realistic settings. The correlated methodologies are utilized in this case as  high-accuracy drivers for quantum part of the  QM/MM and Embedded Clusters formalisms.  This functionality  provides a unique opportunity of  excited-state studies of molecular systems in solution and localized excited states for materials. Another advantage of using TCE generated CC codes  is a possibility of utilizing  various types of reference functions for closed- and open-shell systems including RHF, ROHF, UHF, and DFT references. Recently developed solvers for the EOMCC theory enable one to deal with excited states of highly diversified configurational structure.
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=Extensive QM/MM Capabilities Are Seamlessly Integrated=
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The new QM/MM module provides a seamless integration between molecular mechanics and most quantum-mechanical theories in NWChem. It boasts an extensive array of capabilities for comprehensive description of large molecular systems for chemistry and biology, including [[Qmmm_sp_energy|ground]] and [[QMMM_Excited_States|excited state]] calculations, [[Qmmm_sp_property|properties]], efficient [[Qmmm_optimization|large scale optimizations]], [[Qmmm_NEB_Calculations|reaction pathways]], [[QMMM_Dynamics|dynamics]], and [[QMMM_Free_Energy|free energy]].
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<center><gallery widths=170px perrow=3 right middle >
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File:Large.png|<small>''[http://jcp.aip.org/resource/1/jcpsa6/v127/i5/p051102_s1 Free energy calculations for chloroform and OH- reaction in aqueous solutions ]''</small>
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File:Active-site.png |<small>''[http://pubs.acs.org/doi/full/10.1021/jp074853q Studying catalytic of mechanism of protein kinase]''</small>
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File:QMMM-excited-states.png|<small>''[http://jcp.aip.org/resource/1/jcpsa6/v125/i21/p211101_s1 Studying excited states in DNA]''</small>
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</gallery></center>
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=High Accuracy Is Achievable for Molecular Properties and Excited States=
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[[File:C60.png|right|200px|Excellent agreement between dipole polarizabilities of C60 calculated with NWChem using LR-CCSD and experimental values]]
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With the recently developed linear-response coupled-cluster module, high-precision calculations for static and dynamic molecular properties are possible.  Several levels of theory have been implemented including models based on singles and doubles (LR-CCSD) as well as more sophisticated theories based on the singles, doubles, and triples (LR-CCSDT).  The recent  studies of static/dynamic polarizabilities  for [http://dx.doi.org/10.1063/1.2772853 polyacenes] and [http://dx.doi.org/10.1063/1.3028541 C60 molecule] clearly demonstrate a great potential of the LR-CC theory in retaining the essential part of the correlation effects.  The LR-CCSD approach enables also highly-accurate estimates of the [http://dx.doi.org/10.1063/1.3134744  static hyperpolarizabilities for systems where low-rank methods fail].
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=Scalable Plane Wave Has Exact Exchange=
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[[File:Bylaska_figure1b.JPG|left|150px|Unique relativistic Car-Parrinello simulations uranyl in water show excellent agreement with available experimental data.]]
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[[File:Bylaska-Figure3.PNG|right|200px|caption]]
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The NWChem highly scalable Plane-Wave module now enables users to use exact exchange and the Self-Interaction Correction (SIC) within its framework for complex molecular, liquid, and solid-state systems. In addition, great improvements in parallel performance allow users to study larger systems at longer time scales with a faster time-to-solution. Scaling to 24,000 processors has been demonstrated for a 160 atom hematite cluster using density functional theory with exact exchange.
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NWChem’s Car-Parrinello simulation capability, incorporating relativistic effects, was used to [http://jcp.aip.org/resource/1/jcpsa6/v128/i12/p124507_s1 model the behavior of uranium in complex solution environments] and on iron-oxide surfaces as well as clay layers.
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=Molecular Dynamics of Complex Biomolecular Systems=
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[[File:OprF.png|right|200px|Outer membrane OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane.]]
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The Molecular Dynamics (MD) module of NWChem is designed for the simulation of biomolecular systems, with special features that facilitate the setup of complex systems such as memprane proteins embedded in complex microbial membranes consisting. These capabilities have been used to perform the first ever computer simulations of outer membrane proteins in lipopolysaccharide membranes, in a study of the [http://dx.doi.org/10.1002/prot.22165 OprF outer membrane protein of Pseudomonas aeruginosa.]
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Revision as of 15:59, 31 May 2016

NWChem Related Publications

NWChem-related publications are publications detected via a Web-based search that either acknowledge or use NWChem.

2016 publications

  • Abburu S, V Venkatraman, and BK Alsberg. 2016. "TD-DFT Based Fine-Tuning of Molecular Excitation Energies Using Evolutionary Algorithms." RSC Advances 6:3661-3670.
  • Aprà E and K Kowalski. 2016. "Implementation of High-Order Multireference Coupled-Cluster Methods on Intel Many Integrated Core Architecture." Journal of Chemical Theory and Computation 12:1129-1138.
  • Aslan M, JBA Davis, and RL Johnston. 2016. "Global Optimization of Small Bimetallic Pd-Co Binary Nanoalloy Clusters: A Genetic Algorithm Approach at the DFT Level." Physical Chemistry Chemical Physics 18:6676-6682.
  • Brémond É, M Savarese, NQ Su, ÁJ Pérez-Jiménez, X Xu, JC Sancho-García, and C Adamo. 2016. "Benchmarking Density Functionals on Structural Parameters of Small-/Medium-Sized Organic Molecules." Journal of Chemical Theory and Computation 12:459-465.
  • Brown DML, H Cho, and WA de Jong. 2016. "Bridging Experiment and Theory: A Template for Unifying NMR Data and Electronic Structure Calculations." Journal of Cheminformatics Article no. 8.
  • Brůhová Michalčíková R, K Dryahina, and P Španěl. 2016. "SIFT-MS Quantification of Several Breath Biomarkers of Inflammatory Bowel Disease, IBD: A Detailed Study of the Ion Chemistry." International Journal of Mass Spectrometry 396:35-41.
  • Collins RN, KM Rosso, AL Rose, CJ Glover, and T David Waite. 2016. "An in situ XAS Study of Ferric Iron Hydrolysis and Precipitation in the Presence of Perchlorate, Nitrate, Chloride and Sulfate." Geochimica et Cosmochimica Acta 177:150-169.
  • Chow E, X Liu, S Misra, M Dukhan, M Smelyanskiy, JR Hammond, Y Du, X-K Liao, and P Dubey. 2016. "Scaling up Hartree-Fock Calculations on Tianhe-2." International Journal of High Performance Computing Applications 30:85-102.
  • Chwee TS, GS Lim, ZC Wong, MB Sullivan, and WY Fan. 2016. "Rapid Intersystem Crossings in Anti Bimanes." Physical Chemistry Chemical Physics 18:7404-7413.
  • Cochrane B and FY Naumkin. 2016. "Reshaping and Linking of Molecules in Ion-Pair Traps." Chemical Physics Letters 643:137-141.
  • Deb N, B Li, M Skoda, S Rogers, Y Sun, X Gong, A Karim, BG Sumpter, and DG Bucknall. 2016. "Harnessing Structure–Property Relationships for Poly(alkyl thiophene)–Fullerene Derivative Thin Films to Optimize Performance in Photovoltaic Devices." Advanced Functional Materials 26:1908-1920.
  • Fang Z, P Zetterholm, and DA Dixon. 2016. "1,2-Ethanediol and 1,3-Propanediol Conversions over (MO3)3 (M = Mo, W) Nanoclusters: A Computational Study." The Journal of Physical Chemistry A 120:1897-1907.
  • Fischer SA, TW Ueltschi, PZ El-Khoury, AL Mifflin, WP Hess, H-F Wang, CJ Cramer, and N Govind. 2016. "Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C–H Region of DMSO as a Case Study." The Journal of Physical Chemistry B 120:1429-1436.
  • Gálvez O, M Teresa Baeza-Romero, M Sanz, and LF Pacios. 2016. "A Theoretical Study on the Reaction of Ozone with Aqueous Iodide." Physical Chemistry Chemical Physics 18:7651-7660.
  • Gao M, AJ Misquitta, LHN Rimmer, and MT Dove. 2016. "Molecular Dynamics Simulation Study of Various Zeolitic Imidazolate Framework Structures." Dalton Transactions 45:4289-4302.
  • Ghuman KK, LB Hoch, P Szymanski, JYY Loh, NP Kherani, MA El-Sayed, GA Ozin, and CV Singh. 2016. "Photoexcited Surface Frustrated Lewis Pairs for Heterogeneous Photocatalytic CO2 Reduction." Journal of the American Chemical Society 138:1206-1214.
  • Grimmel S, G Schoendorff, and AK Wilson. 2016. "Gauging the Performance of Density Functionals for Lanthanide-Containing Molecules." Journal of Chemical Theory and Computation 12:1259-1266.
  • Haghdani S, P-O Åstrand, and H Koch. 2016. "Optical Rotation from Coupled Cluster and Density Functional Theory: The Role of Basis Set Convergence." Journal of Chemical Theory and Computation 12:535-548.
  • Hu H-S, Y-F Zhao, JR Hammond, EJ Bylaska, E Aprà, HJJ van Dam, J Li, N Govind, and K Kowalski. 2016. "Theoretical Studies of the Global Minima and Polarizabilities of Small Lithium Clusters." Chemical Physics Letters 644:235-242.
  • Huang W and J-L Liao. 2016. "Catalytic Mechanism of the Maltose Transporter Hydrolyzing ATP." Biochemistry 55:224-231.
  • Jacobs MJ, G Schneider, and KG Blank. 2016. "Mechanical Reversibility of Strain-Promoted Azide–Alkyne Cycloaddition Reactions." Angewandte Chemie International Edition 55:2899-2902.
  • Karadakov PB. 2016. "Do Large Polycyclic Aromatic Hydrocarbons and Graphene Bend? How Popular Theoretical Methods Complicate Finding the Answer to This Question." Chemical Physics Letters 646:190-196.
  • Khrenova MG, ED Kots, AM Kulakova, and IV Polyakov. 2016. "Modeling GTP Hydrolysis in RasGAP Protein Complex." Moscow University Chemistry Bulletin 71:21-24.
  • Kladnik G, M Puppin, M Coreno, M de Simone, L Floreano, A Verdini, A Morgante, D Cvetko, and A Cossaro. 2016. "Ultrafast Charge Transfer Pathways through a Prototype Amino-Carboxylic Molecular Junction." Nano Letters 16:1955-1959.
  • Köç M, Y Zorlu, U İşci, S Berber, V Ahsen, and F Dumoulin. 2016. "A Library of Dimeric and Trimeric Phthalonitriles Linked by a Single Aromatic Ring: Comparative Structural and DFT Investigations." CrystEngComm 18:1416-1426.
  • Kozlov MI, VV Poddubnyy, IO Glebov, AS Belov, and DV Khokhlov. 2016. "Ab initio Calculation of Excitonic Hamiltonian of Light-Harvesting Complex LH1 of Thermochromatium tepidum." Chemical Physics Letters 645:48-52.
  • Kuisma MJ, AM Lundin, K Moth-Poulsen, P Hyldgaard, and P Erhart. 2016. "Comparative Ab-Initio Study of Substituted Norbornadiene-Quadricyclane Compounds for Solar Thermal Storage." The Journal of Physical Chemistry C 120:3635-3645.
  • Kumar RP, L Roopa, U Nongthomba, MM Sudheer Mohammed, and N Kulkarni. 2016. "Docking, Molecular Dynamics and QM/MM Studies to Delineate the Mode of Binding of CucurbitacinE to F-actin." Journal of Molecular Graphics and Modelling 63:29-37.
  • Lv J, J Zhang, and D Wang. 2016. "A Multi-Level Quantum Mechanics and Molecular Mechanics Study of SN2 Reaction at Nitrogen: NH2Cl + OH- in Aqueous Solution." Physical Chemistry Chemical Physics 18:6146-6152.
  • Manaa MR, LE Fried, and I-FW Kuo. 2016. "Determination of Enthalpies of Formation of Energetic Molecules with Composite Quantum Chemical Methods." Chemical Physics Letters 648:31-35.
  • Mancuso R, DS Raut, N Marino, G De Luca, C Giordano, S Catalano, I Barone, S Andò, and B Gabriele. 2016. "A Palladium-Catalyzed Carbonylation Approach to Eight-Membered Lactam Derivatives with Antitumor Activity." Chemistry – A European Journal 22:3053-3064.
  • Mendoza-Huizar LH, G Salgado-Morán, R Ramirez-Tagle, and D Glossman-Mitnik. 2016. "A Theoretical Quantum Study of the Intramolecular Interactions and Chemical Reactivity of Polymorphs A and B of Famotidine in the Gas, DMSO, and Aqueous Phases." Computational and Theoretical Chemistry 1075:54-62.
  • Moore JE and L Jensen. 2016. "Orbital Renormalization Effects on the Coupling between Molecular Excitations and Plasmons." The Journal of Physical Chemistry C 120:5659-5666.
  • Mosquera MA, CH Borca, MA Ratner, and GC Schatz. 2016. "Connection between Hybrid Functionals and Importance of the Local Density Approximation." The Journal of Physical Chemistry A 120:1605-1612.
  • Nemukhin AV, AM Kulakova, SV Lushchekina, AY Ermilov, and SD Varfolomeev. 2016. "Modeling Chemical Transformations at the Active Sites of Cholinesterases by Quantum-Based Simulations." Moscow University Chemistry Bulletin 70:274-277.
  • Pérez-Soto R, SA Vázquez, and E Martínez-Núñez. 2016. "Photodissociation of Acryloyl Chloride at 193 nm: Interpretation of the Product Energy Distributions, and New Elimination Pathways." Physical Chemistry Chemical Physics 18:5019-5026.
  • Perlikowska R, J Piekielna, L Gentilucci, R De Marco, MC Cerlesi, G Calo, R Artali, C Tömböly, A Kluczyk, and A Janecka. 2016. "Synthesis of Mixed MOR/KOR Efficacy Cyclic Opioid Peptide Analogs with Antinociceptive Activity after Systemic Administration." European Journal of Medicinal Chemistry 109:276-286.
  • Petitjean L, R Gagne, ES Beach, D Xiao, and PT Anastas. 2016. "Highly Selective Hydrogenation and Hydrogenolysis Using a Copper-Doped Porous Metal Oxide Catalyst." Green Chemistry 18:150-156.
  • Rippy KC, EV Bukovsky, TT Clikeman, Y-S Chen, G-L Hou, X-B Wang, AA Popov, OV Boltalina, and SH Strauss. 2016. "Copper Causes Regiospecific Formation of C4F8-Containing Six-Membered Rings and Their Defluorination/Aromatization to C4F4-Containing Rings in Triphenylene/1,4-C4F8I2 Reactions." Chemistry – A European Journal 22:874-877.
  • Savoy ES and FA Escobedo. 2016. "Molecular Simulation of the Effects of Humidity and of Interfacial Si- and B-Hydroxyls on the Adhesion Energy between Glass Plates." Journal of Colloid and Interface Science 465:233-241.
  • Sergentu D-C, D Teze, A Sabatié-Gogova, C Alliot, N Guo, F Bassal, I Da Silva, D Deniaud, R Maurice, J Champion, N Galland, and G Montavon. 2016. "Advances on the Determination of the Astatine Pourbaix Diagram: Predomination of AtO(OH)2− over At− in Basic Conditions." Chemistry – A European Journal 22:2964-2971.
  • Singh G, AC Chamberlin, HR Zhekova, SY Noskov, and DP Tieleman. 2016. "Two-Dimensional Potentials of Mean Force of Nile Red in Intact and Damaged Model Bilayers. Application to Calculations of Fluorescence Spectra." Journal of Chemical Theory and Computation 12:364-371.
  • Soniat M, G Pool, L Franklin, and SW Rick. 2016. "Ion Association in Aqueous Solution." Fluid Phase Equilibria 407:31-38.
  • Soriano-Agueda LA, C Ortega-Moo, J Garza, JA Guevara-García, and R Vargas. 2016. "Formation of Reactive Oxygen Species by Vanadium Complexes." Computational and Theoretical Chemistry 1077:99-105.
  • Sun H, S Zhang, C Zhong, and Z Sun. 2016. "Theoretical Study of Excited States of DNA Base Dimers and Tetramers Using Optimally Tuned Range-Separated Density Functional Theory." Journal of Computational Chemistry 37:684-693.
  • Swenson NK, MA Ratner, and EA Weiss. 2016. "Computational Study of the Influence of the Binding Geometries of Organic Ligands on the Photoluminescence Quantum Yield of CdSe Clusters." The Journal of Physical Chemistry C 120:6859-6868.
  • Tainter CJ and GC Schatz. 2016. "Reactive Force Field Modeling of Zinc Oxide Nanoparticle Formation." The Journal of Physical Chemistry C 120:2950-2961.
  • Tan M-L, BS Perrin, S Niu, Q Huang, and T Ichiye. 2016. "Protein Dynamics and the All-Ferrous [Fe4S4] Cluster in the Nitrogenase Iron Protein." Protein Science 25:12-18.
  • Ueltschi TW, SA Fischer, E Aprà, AN Tarnovsky, N Govind, PZ El-Khoury, and WP Hess. 2016. "Time-Domain Simulations of Transient Species in Experimentally Relevant Environments." The Journal of Physical Chemistry A 120:556-561.
  • Valiev M, SHM Deng, and X-B Wang. 2016. "How Anion Chaotrope Changes the Local Structure of Water: Insights from Photoelectron Spectroscopy and Theoretical Modeling of SCN– Water Clusters." The Journal of Physical Chemistry B 120:1518-1525.
  • Verma P, WD Derricotte, and FA Evangelista. 2016. "Predicting Near Edge X-ray Absorption Spectra with the Spin-Free Exact-Two-Component Hamiltonian and Orthogonality Constrained Density Functional Theory." Journal of Chemical Theory and Computation 12:144-156.
  • Wang J, L Liu, and AK Wilson. 2016. "Oxidative Cleavage of the β-O-4 Linkage of Lignin by Transition Metals: Catalytic Properties and the Performance of Density Functionals." The Journal of Physical Chemistry A 120:737-746.
  • Webre WA, JP Hill, Y Matsushita, PA Karr, K Ariga, and F D'Souza. 2016. "Anion Binding, Electrochemistry and Solvatochromism of β-Brominated Oxoporphyrinogens." Dalton Transactions 45:4006-4016.
  • Yao H, Q Dai, and Z You. 2016. "Molecular Dynamics Simulation of Physicochemical Properties of the Asphalt Model." Fuel 164:83-93.
  • Yoo K, AM Dive, S Kazemiabnavi, S Banerjee, and P Dutta. 2016. "Effects of Operating Temperature on the Electrical Performance of a Li-air Battery Operated with Ionic Liquid Electrolyte." Electrochimica Acta 194:317-329.
  • Zhang J, AL Weisman, P Saitta, and RA Friesner. 2016. "Efficient Simulation of Large Materials Clusters Using the Jaguar Quantum Chemistry Program: Parallelization and Wavefunction Initialization." International Journal of Quantum Chemistry 116:357-368.
  • Zhang J, L Yang, J Xie, and WL Hase. 2016. "Microsolvated F–(H2O) + CH3I SN2 Reaction Dynamics. Insight into the Suppressed Formation of Solvated Products." The Journal of Physical Chemistry Letters 7:660-665.
  • Zhang Y, DA Williams, SA Zaidi, Y Yuan, A Braithwaite, EJ Bilsky, WL Dewey, HI Akbarali, JM Streicher, and DE Selley. 2016. "17-Cyclopropylmethyl-3,14β-dihydroxy-4,5α-epoxy-6β-(4′-pyridylcarboxamido)morphinan (NAP) Modulating the Mu Opioid Receptor in a Biased Fashion." ACS Chemical Neuroscience 7:297-304.
  • Zheng L, NF Polizzi, AR Dave, A Migliore, and DN Beratan. 2016. "Where Is the Electronic Oscillator Strength? Mapping Oscillator Strength across Molecular Absorption Spectra." The Journal of Physical Chemistry A 120:1933-1943.


A full list of research publications that utilized NWChem can be found here.