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Science

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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, [[media:nwchem_actinides.pdf | 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.pnl.gov/capabilities/computing/nwchem/pubs.jsp here].
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We highlight NWChem publications from all our users. 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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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 functional 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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'''2016'''
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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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<ul><li>Abburu S, V Venkatraman, and BK Alsberg. 2016. "TD-DFT Based Fine-Tuning of Molecular Excitation Energies Using Evolutionary Algorithms." <em>RSC Advances</em> 6:3661-3670.</li>
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<li>Adrjan B, W Makulski, K Jackowski, TB Demissie, K Ruud, A Antušek, and M Jaszuński. 2016. "NMR Absolute Shielding Scale and Nuclear Magnetic Dipole Moment of <sup>207</sup>Pb." <em>Physical Chemistry Chemical Physics</em> 18:16483-16490.</li>
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<li>Al-Balushi RA, A Haque, M Jayapal, MK Al-Suti, J Husband, MS Khan, OF Koentjoro, KC Molloy, JM Skelton, and PR Raithby. 2016. "Experimental and Theoretical Investigation for the Level of Conjugation in Carbazole-Based Precursors and Their Mono-, Di-, and Polynuclear Pt(II) Complexes." <em>Inorganic Chemistry</em> 55:6465-6480.</li>
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<li>Aprà E and K Kowalski. 2016. "Implementation of High-Order Multireference Coupled-Cluster Methods on Intel Many Integrated Core Architecture." <em>Journal of Chemical Theory and Computation</em> 12:1129-1138.</li>
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<li>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." <em>Physical Chemistry Chemical Physics</em> 18:6676-6682.</li>
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<li>Ayed T, J Pilmé, D Tézé, F Bassal, J Barbet, M Chérel, J Champion, R Maurice, G Montavon, and N Galland. 2016. "<sup>211</sup>At-Labeled Agents for Alpha-Immunotherapy: On the <em>in vivo</em> Stability of Astatine-Agent Bonds." <em>European Journal of Medicinal Chemistry</em> 116:156-164.</li>
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<li>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." <em>Journal of Chemical Theory and Computation</em> 12:459-465.</li>
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<li>Brown DML, H Cho, and WA de Jong. 2016. "Bridging Experiment and Theory: A Template for Unifying NMR Data and Electronic Structure Calculations." <em>Journal of Cheminformatics</em> Article no. 8.</li>
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<li>Brückner C and B Engels. 2016. "A Theoretical Description of Charge Reorganization Energies in Molecular Organic P-Type Semiconductors." <em>Journal of Computational Chemistry</em> 37:1335-1344.</li>
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<li>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." <em>International Journal of Mass Spectrometry</em> 396:35-41.</li>
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<li>Boschen JS, J Lee, TL Windus, JW Evans, and D-J Liu. 2016. "Size Dependence of S-bonding on (111) Facets of Cu Nanoclusters." <em>The Journal of Physical Chemistry C</em> 120:10268-10274.</li>
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<li>Brabec J, C Yang, E Epifanovsky, AI Krylov, and E Ng. 2016. "Reduced-Cost Sparsity-Exploiting Algorithm for Solving Coupled-Cluster Equations." <em>Journal of Computational Chemistry</em> 37:1059-1067.</li>
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<li>Bristow JK, KL Svane, D Tiana, JM Skelton, JD Gale, and A Walsh. 2016. "Free Energy of Ligand Removal in the Metal–Organic Framework UiO-66." <em>The Journal of Physical Chemistry C</em> 120:9276-9281.</li>
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<li>Campo JMd. 2016. "B88 Exchange Functional Recovering the Local Spin Density Linear Response." <em>Theoretical Chemistry Accounts</em> 135: Article no. 179.</li>
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<li>Carmona-Espíndola J, JL Gázquez, A Vela, and SB Trickey. 2016. "Global Hybrid Exchange Energy Functional with Correct Asymptotic Behavior of the Corresponding Potential." <em>Theoretical Chemistry Accounts</em> 135:Article no. 120.</li>
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<li>Carrillo J-MY, Z Seibers, R Kumar, MA Matheson, JF Ankner, M Goswami, K Bhaskaran-Nair, WA Shelton, BG Sumpter, and SM Kilbey, II. 2016. "Petascale Simulations of the Morphology and the Molecular Interface of Bulk Heterojunctions." <em>ACS Nano</em> 10:7008-7022.</li>
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<li>Chen W, G-H Chen, D Wu, and Q Wang. 2016. "BNg<sub>3</sub>F<sub>3</sub>: The First Three Noble Gas Atoms Inserted into Mono-Centric Neutral Compounds - a Theoretical Study." <em>Physical Chemistry Chemical Physics</em> 18:17534-17545.</li>
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<li>Collins RN, KM Rosso, AL Rose, CJ Glover, and T David Waite. 2016. "An <em>in situ</em> XAS Study of Ferric Iron Hydrolysis and Precipitation in the Presence of Perchlorate, Nitrate, Chloride and Sulfate." <em>Geochimica et Cosmochimica Acta</em> 177:150-169.</li>
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<li>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." <em>International Journal of High Performance Computing Applications</em> 30:85-102.</li>
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<li>Chwee TS, GS Lim, ZC Wong, MB Sullivan, and WY Fan. 2016. "Rapid Intersystem Crossings in <em>Anti</em> Bimanes." <em>Physical Chemistry Chemical Physics</em> 18:7404-7413.</li>
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<li>Cochrane B and FY Naumkin. 2016. "Reshaping and Linking of Molecules in Ion-Pair Traps." <em>Chemical Physics Letters</em> 643:137-141.</li>
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<li>Dau PD, D Rios, Y Gong, MC Michelini, J Marçalo, DK Shuh, M Mogannam, MJ Van Stipdonk, TA Corcovilos, JK Martens, G Berden, J Oomens, B Redlich, and JK Gibson. 2016. "Synthesis and Hydrolysis of Uranyl, Neptunyl, and Plutonyl Gas-Phase Complexes Exhibiting Discrete Actinide–Carbon Bonds." <em>Organometallics</em> 35:1228-1240.</li>
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<li>Douhaya YV, VV Barkaline, and A Tsakalof. 2016. "Computer-Simulation-Based Selection of Optimal Monomer for Imprinting of Tri-O-Acetyl Adenosine in a Polymer Matrix: Calculations for Benzene Solution." <em>Journal of Molecular Modeling</em> 22:Article no. 154.</li>
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<li>Duanmu K, O Roberto-Neto, FBC Machado, JA Hansen, J Shen, P Piecuch, and DG Truhlar. 2016. "Geometries, Binding Energies, Ionization Potentials, and Electron Affinities of Metal Clusters: Mg<em><sub>n</sub></em><sup>0, ± 1</sup>, <em>n</em> = 1–7." <em>The Journal of Physical Chemistry C</em> 120:13275-13286.</li>
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<li>Duignan TJ and J Autschbach. 2016. "Impact of the Kohn–Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide Complexes." <em>Journal of Chemical Theory and Computation</em> 12:3109-3121.</li>
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<li>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." <em>Advanced Functional Materials</em> 26:1908-1920.</li>
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<li>Ermanis K, KEB Parkes, T Agback, and JM Goodman. 2016. "Expanding DP4: Application to Drug Compounds and Automation." <em>Organic &amp; Biomolecular Chemistry</em> 14:3943-3949.</li>
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<li>Evtimova J, E Drioli, and G De Luca. 2016. "A Density Functional Theory Study of Hydrogen Occupation in VNiTi Alloys Used for Dense Metal Membranes." <em>Journal of Alloys and Compounds</em> 665:225-230.</li>
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<li>Fang W, J Chen, M Rossi, Y Feng, X-Z Li, and A Michaelides. 2016. "Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs." <em>The Journal of Physical Chemistry Letters</em> 7:2125-2131.</li>
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<li>Fang Z, P Zetterholm, and DA Dixon. 2016. "1,2-Ethanediol and 1,3-Propanediol Conversions over (MO<sub>3</sub>)<sub>3</sub> (M = Mo, W) Nanoclusters: A Computational Study." <em>The Journal of Physical Chemistry A</em> 120:1897-1907.</li>
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<li>Fayon P and A Trewin. 2016. "Formation Mechanism of Ultra Porous Framework Materials." <em>Physical Chemistry Chemical Physics</em> 18:16840-16847.</li>
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<li>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." <em>The Journal of Physical Chemistry B</em> 120:1429-1436.</li>
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<li>Fischer SA, CJ Cramer, and N Govind. 2016. "Excited-State Absorption from Real-Time Time-Dependent Density Functional Theory: Optical Limiting in Zinc Phthalocyanine." <em>The Journal of Physical Chemistry Letters</em> 7:1387-1391.</li>
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<li>Fornari RP, J Aragó, and A Troisi. 2016. "Exciton Dynamics in Phthalocyanine Molecular Crystals." <em>The Journal of Physical Chemistry C</em> 120:7987-7996.</li>
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<li>Fosso-Tande J, T-S Nguyen, G Gidofalvi, and AE DePrince, III. 2016. "Large-Scale Variational Two-Electron Reduced-Density-Matrix-Driven Complete Active Space Self-Consistent Field Methods." <em>Journal of Chemical Theory and Computation</em> 12:2260-2271.</li>
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<li>Fox SJ, MHUT Fazil, C Dhand, M Venkatesh, ETL Goh, S Harini, C Eugene, RR Lim, S Ramakrishna, SS Chaurasia, RW Beuerman, CS Verma, NK Verma, XJ Loh, and R Lakshminarayanan. 2016. "Insight into Membrane Selectivity of Linear and Branched Polyethylenimines and Their Potential as Biocides for Advanced Wound Dressings." <em>Acta Biomaterialia</em> 37:155-164.</li>
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<li>Fujii M, W Shin, T Yasuda, and K Yamashita. 2016. "Photon-Absorbing Charge-Bridging States in Organic Bulk Heterojunctions Consisting of Diketopyrrolopyrrole Derivatives and PCBM." <em>Physical Chemistry Chemical Physics</em> 18:9514-9523.</li>
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<li>Gaines E, K Maisuria, and D Di Tommaso. 2016. "The Role of Solvent in the Self-Assembly of <em>m</em>-Aminobenzoic Acid: A Density Functional Theory and Molecular Dynamics Study." <em>CrystEngComm</em> 18:2937-2948.</li>
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<li>Gálvez O, M Teresa Baeza-Romero, M Sanz, and LF Pacios. 2016. "A Theoretical Study on the Reaction of Ozone with Aqueous Iodide." <em>Physical Chemistry Chemical Physics</em> 18:7651-7660.</li>
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<li>Gao M, AJ Misquitta, LHN Rimmer, and MT Dove. 2016. "Molecular Dynamics Simulation Study of Various Zeolitic Imidazolate Framework Structures." <em>Dalton Transactions</em> 45:4289-4302.</li>
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<li>Ghambarian M, Z Azizi, and M Ghashghaee. 2016. "Diversity of Monomeric Dioxo Chromium Species in Cr/Silicalite-2 Catalysts: A Hybrid Density Functional Study." <em>Computational Materials Science</em> 118:147-154.</li>
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<li>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 CO<sub>2</sub> Reduction." <em>Journal of the American Chemical Society</em> 138:1206-1214.</li>
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<li>Göttle AJ, F Alary, M Boggio-Pasqua, IM Dixon, J-L Heully, A Bahreman, SHC Askes, and S Bonnet. 2016. "Pivotal Role of a Pentacoordinate <sup>3</sup>MC State on the Photocleavage Efficiency of a Thioether Ligand in Ruthenium(II) Complexes: A Theoretical Mechanistic Study." <em>Inorganic Chemistry</em> 55:4448-4456.</li>
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<li>Götz DA, A Shayeghi, RL Johnston, P Schwerdtfeger, and R Schäfer. 2016. "Structural Evolution and Metallicity of Lead Clusters." <em>Nanoscale</em> 8:11153-11160.</li>
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<li>Grimmel S, G Schoendorff, and AK Wilson. 2016. "Gauging the Performance of Density Functionals for Lanthanide-Containing Molecules." <em>Journal of Chemical Theory and Computation</em> 12:1259-1266.</li>
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<li>Gunaratne KDD, V Prabhakaran, A Andersen, GE Johnson, and J Laskin. 2016. "Charge Retention of Soft-Landed Phosphotungstate Keggin Anions on Self-Assembled Monolayers." <em>Physical Chemistry Chemical Physics</em> 18:9021-9028.</li>
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<li>Gupta T and G Rajaraman. 2016. "Modelling Spin Hamiltonian Parameters of Molecular Nanomagnets." <em>Chemical Communications</em> 52:8972-9008.</li>
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<li>Haghdani S, P-O Åstrand, and H Koch. 2016. "Optical Rotation from Coupled Cluster and Density Functional Theory: The Role of Basis Set Convergence." <em>Journal of Chemical Theory and Computation</em> 12:535-548.</li>
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<li>Hermann G, V Pohl, JC Tremblay, B Paulus, H-C Hege, and A Schild. 2016. "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data." <em>Journal of Computational Chemistry</em> 37:1511-1520.</li>
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<li>Hey JC, LC Smeeton, MT Oakley, and RL Johnston. 2016. "Isomers and Energy Landscapes of Perchlorate–Water Clusters and a Comparison to Pure Water and Sulfate–Water Clusters." <em>The Journal of Physical Chemistry A</em> 120:4008-4015.</li>
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<li>Hosseini Lavasani SM, H Nejat Pishkenari, and A Meghdari. 2016. "Mechanism of 1,12-Dicarba-closo-dodecaborane Mobility on Gold Substrate as a Nanocar Wheel." <em>The Journal of Physical Chemistry C</em> 120:14048-14058.</li>
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<li>Hou G-L, M Valiev, and X-B Wang. 2016. "Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications." <em>The Journal of Physical Chemistry A</em> 120:2342-2349.</li>
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<li>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." <em>Chemical Physics Letters</em> 644:235-242.</li>
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<li>Huang W and J-L Liao. 2016. "Catalytic Mechanism of the Maltose Transporter Hydrolyzing ATP." <em>Biochemistry</em> 55:224-231.</li>
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<li>Jacobs MJ, G Schneider, and KG Blank. 2016. "Mechanical Reversibility of Strain-Promoted Azide–Alkyne Cycloaddition Reactions." <em>Angewandte Chemie International Edition</em> 55:2899-2902.</li>
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<li>Janocha S, Y Carius, M Hutter, CRD Lancaster, and R Bernhardt. 2016. "Crystal Structure of CYP106A2 in Substrate-Free and Substrate-Bound Form." <em>ChemBioChem</em> 17:852-860.</li>
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<li>Jia C, A Migliore, N Xin, S Huang, J Wang, Q Yang, S Wang, H Chen, D Wang, B Feng, Z Liu, G Zhang, D-H Qu, H Tian, MA Ratner, HQ Xu, A Nitzan, and X Guo. 2016. "Covalently Bonded Single-Molecule Junctions with Stable and Reversible Photoswitched Conductivity." <em>Science</em> 352:1443-1445.</li>
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<li>Jindal N, V Lotrich, E Deumens, and BA Sanders. 2016. "Exploiting GPUs with the Super Instruction Architecture." <em>International Journal of Parallel Programming</em> 44:309-324.</li>
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<li>Karadakov PB. 2016. "Do Large Polycyclic Aromatic Hydrocarbons and Graphene Bend? How Popular Theoretical Methods Complicate Finding the Answer to This Question." <em>Chemical Physics Letters</em> 646:190-196.</li>
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<li>Kayanuma M, M Shoji, M Yohda, M Odaka, and Y Shigeta. 2016. "Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study." <em>The Journal of Physical Chemistry B</em> 120:3259-3266.Kaydashev V, P Ferrari, C Heard, E Janssens, RL Johnston, and P Lievens. 2016. "Optical Absorption of Small Palladium-Doped Gold Clusters." <em>Particle &amp; Particle Systems Characterization</em> 33:364-372.</li>
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<li>Kelley MP, P Yang, SB Clark, and AE Clark. 2016. "Structural and Thermodynamic Properties of the Cm<sup>III</sup> Ion Solvated by Water and Methanol." <em>Inorganic Chemistry</em> 55:4992-4999.Khetrapal NS, T Jian, R Pal, GV Lopez, S Pande, L-S Wang, and XC Zeng. 2016. "Probing the Structures of Gold-Aluminum Alloy Clusters Au<em><sub>x</sub></em>Al<em><sub>y</sub></em><sup>-</sup>: A Joint Experimental and Theoretical Study." <em>Nanoscale</em> 8:9805-9814.</li>
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<li>Khrenova MG, ED Kots, AM Kulakova, and IV Polyakov. 2016. "Modeling GTP Hydrolysis in RasGAP Protein Complex." <em>Moscow University Chemistry Bulletin</em> 71:21-24.</li>
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<li>Khrenova MG, ED Kots, and AV Nemukhin. 2016. "Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3–RP2." <em>The Journal of Physical Chemistry B</em> 120:3873-3879.</li>
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<li>Khetrapal NS, T Jian, R Pal, GV Lopez, S Pande, L-S Wang, and XC Zeng. 2016. "Probing the Structures of Gold-Aluminum Alloy Clusters Au<em><sub>x</sub></em>Al<em><sub>y</sub></em><sup>-</sup>: A Joint Experimental and Theoretical Study." <em>Nanoscale</em> 8:9805-9814.</li>
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<li>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." <em>Nano Letters</em> 16:1955-1959.</li>
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<li>Kobayashi T, FA Perras, TW Goh, TL Metz, W Huang, and M Pruski. 2016. "DNP-Enhanced Ultrawideline Solid-State NMR Spectroscopy: Studies of Platinum in Metal–Organic Frameworks." <em>The Journal of Physical Chemistry Letters</em> 7:2322-2327.</li>
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<li>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." <em>CrystEngComm</em> 18:1416-1426.</li>
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<li>Koda S, M Fujii, S Hatamiya, and K Yamashita. 2016. "Dipole Analyses for Short-Circuit Current in Organic Photovoltaic Devices of Diketopyrrolopyrrole-Based Donor and PCBM." <em>Theoretical Chemistry Accounts</em> 135:Article no. 115.Kots ED, MG Khrenova, SV Lushchekina, SD Varfolomeev, BL Grigorenko, and AV Nemukhin. 2016. "Modeling the Complete Catalytic Cycle of Aspartoacylase." <em>The Journal of Physical Chemistry B</em> 120:4221-4231.</li>
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<li>Kots ED, MG Khrenova, SV Lushchekina, SD Varfolomeev, BL Grigorenko, and AV Nemukhin. 2016. "Modeling the Complete Catalytic Cycle of Aspartoacylase." <em>The Journal of Physical Chemistry B</em> 120:4221-4231.</li>
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<li>Kozlov MI, VV Poddubnyy, IO Glebov, AS Belov, and DV Khokhlov. 2016. "<em>Ab initio</em> Calculation of Excitonic Hamiltonian of Light-Harvesting Complex LH1 of <em>Thermochromatium tepidum</em>." <em>Chemical Physics Letters</em> 645:48-52.</li>
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<li>Kratz EG, RE Duke, and GA Cisneros. 2016. "Long-Range Electrostatic Corrections in Multipolar/Polarizable QM/MM Simulations." <em>Theoretical Chemistry Accounts</em> 135:Article no. 166.</li>
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<li>Kratz EG, AR Walker, L Lagardère, F Lipparini, J-P Piquemal, and GA Cisneros. 2016. "LICHEM: A QM/MM Program for Simulations with Multipolar and Polarizable Force Fields." <em>Journal of Computational Chemistry</em> 37:1019-1029.</li>
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<li>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." <em>The Journal of Physical Chemistry C</em> 120:3635-3645.</li>
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<li>Kuisma M, A Lundin, K Moth-Poulsen, P Hyldgaard, and P Erhart. 2016. "Optimization of Norbornadiene Compounds for Solar Thermal Storage by First-Principles Calculations." <em>ChemSusChem</em> 9:1786-1794.</li>
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<li>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." <em>Journal of Molecular Graphics and Modelling</em> 63:29-37.</li>
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<li>Li J, G D’Avino, I Duchemin, D Beljonne, and X Blase. 2016. "Combining the Many-Body <em>GW</em> Formalism with Classical Polarizable Models: Insights on the Electronic Structure of Molecular Solids." <em>The Journal of Physical Chemistry Letters</em> 7:2814-2820.</li>
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<li>Lian S, DJ Weinberg, RD Harris, MS Kodaimati, and EA Weiss. 2016. "Subpicosecond Photoinduced Hole Transfer from a CdS Quantum Dot to a Molecular Acceptor Bound Through an Exciton-Delocalizing Ligand." <em>ACS Nano</em> 10:6372-6382.</li>
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<li>Liang R, JMJ Swanson, Y Peng, M Wikström, and GA Voth. 2016. "Multiscale Simulations Reveal Key Features of the Proton-Pumping Mechanism in Cytochrome <em>c</em> Oxidase." <em>Proceedings of the National Academy of Sciences</em> 113:7420-7425.</li>
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<li>Liu X, J Zhang, L Yang, and R Sun. 2016. "Theoretical Studies on F<sup>–</sup> + NH<sub>2</sub>Cl Reaction: Nucleophilic Substitution at Neutral Nitrogen." <em>The Journal of Physical Chemistry A</em> 120:3740-3746.Li X, X Xu, X You, and DG Truhlar. 2016. "Benchmark Calculations for Bond Dissociation Enthalpies of Unsaturated Methyl Esters and the Bond Dissociation Enthalpies of Methyl Linolenate." <em>The Journal of Physical Chemistry A</em> 120:4025-4036.</li>
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<li>Lüthi HP, S Heinen, G Schneider, A Glöss, MP Brändle, RA King, E Pyzer-Knapp, FH Alharbi, and S Kais. 2016. "The Quantum Chemical Search for Novel Materials and the Issue of Data Processing: The InfoMol Project." <em>Journal of Computational Science</em> 15:65-73.</li>
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<li>Lv J, J Zhang, and D Wang. 2016. "A Multi-Level Quantum Mechanics and Molecular Mechanics Study of S<sub>N</sub>2 Reaction at Nitrogen: NH<sub>2</sub>Cl + OH<sup>-</sup> in Aqueous Solution." <em>Physical Chemistry Chemical Physics</em> 18:6146-6152.</li>
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<li>Makhyoun MA, RA Palmer, AA Soayed, HM Refaat, and DE Basher. 2016. "Synthesis, Crystal Structure and Comparative DFT Studies of a 1D Ni(II) Polymeric Complex of 2-Hydroxypyridine-N-oxide." <em>Journal of Chemical Crystallography</em> 46:269-279.</li>
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<li>Manaa MR, LE Fried, and I-FW Kuo. 2016. "Determination of Enthalpies of Formation of Energetic Molecules with Composite Quantum Chemical Methods." <em>Chemical Physics Letters</em> 648:31-35.</li>
 +
<li>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." <em>Chemistry – A European Journal</em> 22:3053-3064.</li>
 +
<li>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." <em>Computational and Theoretical Chemistry</em> 1075:54-62.</li>
 +
<li>Moon J, TK Kim, and J Kim. 2016. "Ground and Low-Lying Excited States of PtCN and PdCN: Theoretical Investigation Including Spin-Orbit Coupling." <em>Theoretical Chemistry Accounts</em> 135:Article no. 127.</li>
 +
<li>Moore JE and L Jensen. 2016. "Orbital Renormalization Effects on the Coupling between Molecular Excitations and Plasmons." <em>The Journal of Physical Chemistry C</em> 120:5659-5666.</li>
 +
<li>Mosquera MA, CH Borca, MA Ratner, and GC Schatz. 2016. "Connection between Hybrid Functionals and Importance of the Local Density Approximation." <em>The Journal of Physical Chemistry A</em> 120:1605-1612.</li>
 +
<li>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." <em>Moscow University Chemistry Bulletin</em> 70:274-277.</li>
 +
<li>Nechay MR, NM Gallup, A Morgenstern, QA Smith, ME Eberhart, and AN Alexandrova. 2016. "Histone Deacetylase 8: Characterization of Physiological Divalent Metal Catalysis." <em>The Journal of Physical Chemistry B</em> 120:5884-5895.</li>
 +
<li>Ng CH, CA Ohlin, S Qiu, C Sun, and B Winther-Jensen. 2016. "Mechanistic Studies of the Photo-Electrochemical Hydrogen Evolution Reaction on Poly(2,2′-bithiophene)." <em>Catalysis Science &amp; Technology</em> 6:3253-3262.</li>
 +
<li>Pacheco-Kato JC, JM del Campo, JL Gázquez, SB Trickey, and A Vela. 2016. "A PW91-Like Exchange with a Simple Analytical Form." <em>Chemical Physics Letters</em> 651:268-273.</li>
 +
<li>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." <em>Physical Chemistry Chemical Physics</em> 18:5019-5026.</li>
 +
<li>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." <em>European Journal of Medicinal Chemistry</em> 109:276-286.</li>
 +
<li>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." <em>Green Chemistry</em> 18:150-156.</li>
 +
<li>Pichugina DA, YG Polynskaya, and NE Kuz'menko. 2016. "Spin and Structural Features of Oxygen Dissociation on Tetrahedral Ag<sub>20</sub> and Ag<sub>19</sub>>Au Clusters." <em>Physical Chemistry Chemical Physics</em> 18:18033-18044.</li>
 +
<li>Piekielna J, R De Marco, L Gentilucci, MC Cerlesi, G Calo, C Tömböly, R Artali, and A Janecka. 2016. "Redoubling the Ring Size of an Endomorphin-2 Analog Transforms a Centrally Acting Mu-Opioid Receptor Agonist into a Pure Peripheral Analgesic." <em>Peptide Science</em> 106:309-317.</li>
 +
<li>Pliss EM, ME Soloviev, IV Tikhonov, DV Loshadkin, and AL Buchachenko. 2016. "Quantum-Chemical Analysis of the Disproportionation of Nitroxyl and Peroxyl Radicals in Oxidizing Organic Compounds." <em>Russian Journal of Physical Chemistry B</em> 10:417-420.</li>
 +
<li>Pruski M, AD Sadow, II Slowing, CL Marshall, P Stair, J Rodriguez, A Harris, GA Somorjai, J Biener, C Matranga, C Wang, JA Schaidle, GT Beckham, DA Ruddy, T Deutsch, SM Alia, C Narula, S Overbury, T Toops, RM Bullock, CHF Peden, Y Wang, MD Allendorf, J Nørskov, and T Bligaard. 2016. "Virtual Special Issue on Catalysis at the U.S. Department of Energy’s National Laboratories." <em>ACS Catalysis</em> 6:3227-3235.</li>
 +
<li>Ramharack P and MES Soliman. 2016. "Zika Virus Drug Targets: A Missing Link in Drug Design and Discovery - a Route Map to Fill the Gap." <em>RSC Advances</em> 6:68719-68731.</li>
 +
<li>Rakhuba MV and IV Oseledets. 2016. "Grid-Based Electronic Structure Calculations: The Tensor Decomposition Approach." <em>Journal of Computational Physics</em> 312:19-30.</li>
 +
<li>Rashev S and DC Moule. 2016. "Theoretical Study on the Vibrational Structure of S<sub>0</sub> Thiophosgene from the Origin to Dissociation." <em>Vibrational Spectroscopy</em> 84:118-126.</li>
 +
<li>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 C<sub>4</sub>F<sub>8</sub>-Containing Six-Membered Rings and Their Defluorination/Aromatization to C<sub>4</sub>F<sub>4</sub>-Containing Rings in Triphenylene/1,4-C<sub>4</sub>F<sub>8</sub>I<sub>2</sub> Reactions." <em>Chemistry – A European Journal</em> 22:874-877.</li>
 +
<li>Ross DAW, PA Scattergood, A Babaei, A Pertegás, HJ Bolink, and PIP Elliott. 2016. "Luminescent Osmium(II) Bi-1,2,3-Triazol-4-yl Complexes: Photophysical Characterisation and Application in Light-Emitting Electrochemical Cells." <em>Dalton Transactions</em> 45:7748-7757.</li>
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<li>Salter-Blanc AJ, EJ Bylaska, MA Lyon, SC Ness, and PG Tratnyek. 2016. "Structure–Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide." <em>Environmental Science &amp; Technology</em> 50:5094-5102.</li>
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<li>Sancho-García JC, M Moral, and AJ Pérez-Jiménez. 2016. "Effect of Cyclic Topology on Charge-Transfer Properties of Organic Molecular Semiconductors: The Case of Cycloparaphenylene Molecules." <em>The Journal of Physical Chemistry C</em> 120:9104-9111.</li>
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<li><span style="font-size:12px"><span style="font-family:arial,sans-serif">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." <em>Journal of Colloid and Interface Science</em> 465:233-241.</span></span></li>
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<li>Scalambra F, M Serrano-Ruiz, S Nahim-Granados, and A Romerosa. 2016. "Ruthenium Complexes Containing 2,2′-Bipyridine and 1,3,5-Triaza-7-phosphaadamantane." <em>European Journal of Inorganic Chemistry</em> 2016:1528-1540.</li>
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<li>Schrauben JN, A Akdag, J Wen, Z Havlas, JL Ryerson, MB Smith, J Michl, and JC Johnson. 2016. "Excitation Localization/Delocalization Isomerism in a Strongly Coupled Covalent Dimer of 1,3-Diphenylisobenzofuran." <em>The Journal of Physical Chemistry A</em> 120:3473-3483.</li>
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<li>Shoji M, H Isobe, J-R Shen, and K Yamaguchi. 2016. "Geometric and Electronic Structures of the Synthetic Mn<strong><sub>4</sub></strong>CaO<strong><sub>4</sub></strong> Model Compound Mimicking the Photosynthetic Oxygen-Evolving Complex." <em>Physical Chemistry Chemical Physics</em> 18:11330-11340.Sergentu D-C, G David, G Montavon, R Maurice, and N Galland. 2016. "Scrutinizing “Invisible” Astatine: A Challenge for Modern Density Functionals." <em>Journal of Computational Chemistry</em> 37:1345-1354.</li>
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<li>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)<strong><sub>2</sub><sup>−</sup></strong> over At<strong><sup>−</sup></strong> in Basic Conditions." <em>Chemistry – A European Journal</em> 22:2964-2971.</li>
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<li>Simm GN and M Reiher. 2016. "Systematic Error Estimation for Chemical Reaction Energies." <em>Journal of Chemical Theory and Computation</em> 12:2762-2773.</li>
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<li>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." <em>Journal of Chemical Theory and Computation</em> 12:364-371.</li>
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<li>Soniat M, G Pool, L Franklin, and SW Rick. 2016. "Ion Association in Aqueous Solution." <em>Fluid Phase Equilibria</em> 407:31-38.</li>
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<li>South C, G Schoendorff, and AK Wilson. 2016. "Dissociation Energy and Electronic Structure of the Low Valent Lanthanide Compound NdF<strong><sup>+</sup></strong>." <em>International Journal of Quantum Chemistry</em> 116:791-794.</li>
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<li>Soriano-Agueda LA, C Ortega-Moo, J Garza, JA Guevara-García, and R Vargas. 2016. "Formation of Reactive Oxygen Species by Vanadium Complexes." <em>Computational and Theoretical Chemistry</em> 1077:99-105.</li>
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<li>Su NQ and X Xu. 2016. "Second-Order Perturbation Theory for Fractional Occupation Systems: Applications to Ionization Potential and Electron Affinity Calculations." <em>Journal of Chemical Theory and Computation</em> 12:2285-2297.</li>
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<li>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." <em>Journal of Computational Chemistry</em> 37:684-693.</li>
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<li>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." <em>The Journal of Physical Chemistry C</em> 120:6859-6868.</li>
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<li>Tainter CJ and GC Schatz. 2016. "Reactive Force Field Modeling of Zinc Oxide Nanoparticle Formation." <em>The Journal of Physical Chemistry C</em> 120:2950-2961.</li>
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<li>TalwelkarShimpi M, S Öberg, L Giri, and VR Pedireddi. 2016. "Experimental and Theoretical Studies of Molecular Complexes of Theophylline with Some Phenylboronic Acids." <em>RSC Advances</em> 6:43060-43068.</li>
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<li>Tan M-L, BS Perrin, S Niu, Q Huang, and T Ichiye. 2016. "Protein Dynamics and the All-Ferrous [Fe<strong><sub>4</sub></strong>S<strong><sub>4</sub></strong>] Cluster in the Nitrogenase Iron Protein." <em>Protein Science</em> 25:12-18.</li>
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<li>Tran VT and QT Tran. 2016. "Quantum Chemical Study of the Low-Lying Electronic States of VSi<strong><sub>3</sub><sup>–/0</sup></strong> Clusters and Interpretation of the Anion Photoelectron Spectrum." <em>The Journal of Physical Chemistry A</em> 120:5950-5957.</li>
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<li>Thorley KJ and C Risko. 2016. "Mapping the Configuration Dependence of Electronic Coupling in Organic Semiconductors." <em>Journal of Materials Chemistry C</em> 4:3825-3832.</li>
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<li>Umadevi P and L Senthilkumar. 2016. "Metal-Interacted Histidine Dimer: An ETS-NOCV and XANES Study." <em>RSC Advances</em> 6:38919-38930.</li>
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<li>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." <em>The Journal of Physical Chemistry A</em> 120:556-561.</li>
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<li>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<strong><sup>–  </sup></strong>Water Clusters." <em>The Journal of Physical Chemistry B</em> 120:1518-1525.</li>
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<li>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." <em>Journal of Chemical Theory and Computation</em> 12:144-156.</li>
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<li>Wagner J, P Deglmann, S Fuchs, M Ciesielski, CA Fleckenstein, and M Döring. 2016. "A Flame Retardant Synergism of Organic Disulfides and Phosphorous Compounds." <em>Polymer Degradation and Stability</em> 129:63-76.</li>
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<li>Wang J, L Liu, and AK Wilson. 2016. "Oxidative Cleavage of the <em>β</em>-O-4 Linkage of Lignin by Transition Metals: Catalytic Properties and the Performance of Density Functionals." <em>The Journal of Physical Chemistry A</em> 120:737-746.</li>
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<li>Webre WA, JP Hill, Y Matsushita, PA Karr, K Ariga, and F D'Souza. 2016. "Anion Binding, Electrochemistry and Solvatochromism of β-Brominated Oxoporphyrinogens." <em>Dalton Transactions</em> 45:4006-4016.</li>
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<li>Woolfson RJ, GA Timco, A Chiesa, IJ Vitorica-Yrezabal, F Tuna, T Guidi, E Pavarini, P Santini, S Carretta, and REP Winpenny. 2016. "[CrF(O<strong><sub>2</sub></strong>C<strong><em><sup>t</sup></em></strong>Bu)<strong><sub>2</sub></strong>]<strong><sub>9</sub></strong>: Synthesis and Characterization of a Regular Homometallic Ring with an Odd Number of Metal Centers and Electrons." <em>Angewandte Chemie International Edition</em> 55:8856-8859.</li>
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<li>Yang Y, Q Wang, W Qiu, H Guo, and F Gao. 2016. "Covalent Immobilization of Cu<strong><sub>3</sub></strong>(btc)<strong><sub>2</sub></strong> at Chitosan–Electroreduced Graphene Oxide Hybrid Film and Its Application for Simultaneous Detection of Dihydroxybenzene Isomers." <em>The Journal of Physical Chemistry C</em> 120:9794-9803.</li>
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<li>Yao H, Q Dai, and Z You. 2016. "Molecular Dynamics Simulation of Physicochemical Properties of the Asphalt Model." <em>Fuel</em> 164:83-93.</li>
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<li>Yan W, A Ramanathan, PD Patel, SK Maiti, BB Laird, WH Thompson, and B Subramaniam. 2016. "Mechanistic Insights for Enhancing Activity and Stability of Nb-Incorporated Silicates for Selective Ethylene Epoxidation." <em>Journal of Catalysis</em> 336:75-84.</li>
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<li>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." <em>Electrochimica Acta</em> 194:317-329.</li>
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<li>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." <em>International Journal of Quantum Chemistry</em> 116:357-368.</li>
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<li>Zhang J, L Yang, J Xie, and WL Hase. 2016. "Microsolvated F<strong><sup>–</sup></strong>(H<strong><sub>2</sub></strong>O) + CH<strong><sub>3</sub></strong>I S<strong><sub>N</sub></strong>2 Reaction Dynamics. Insight into the Suppressed Formation of Solvated Products." <em>The Journal of Physical Chemistry Letters</em> 7:660-665.</li>
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<li>Zhang R, Q He, Y Huang, and X Wang. 2016. "Spectroscopic and QM/MM Investigations of Chloroperoxidase Catalyzed Degradation of Orange G." <em>Archives of Biochemistry and Biophysics</em> 596:1-9.</li>
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<li>Zhang Y, DA Williams, SA Zaidi, Y Yuan, A Braithwaite, EJ Bilsky, WL Dewey, HI Akbarali, JM Streicher, and DE Selley. 2016. "17-Cyclopropylmethyl-3,14<em>β</em>-dihydroxy-4,5<em>α</em>-epoxy-6<em>β</em>-(4′-pyridylcarboxamido)morphinan (NAP) Modulating the Mu Opioid Receptor in a Biased Fashion." <em>ACS Chemical Neuroscience</em> 7:297-304.</li>
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<li>Zhang J, L Yang, and L Sheng. 2016. "Electronic Structure Theory Study of the Microsolvated F<strong><sup>–</sup></strong>(H<strong><sub>2</sub></strong>O) + CH<strong><sub>3</sub></strong>I S<strong><sub>N</sub></strong>2 Reaction." <em>The Journal of Physical Chemistry A</em> 120:3613-3622.</li>
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<li>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." <em>The Journal of Physical Chemistry A</em> 120:1933-1943.</li>
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<li>Zuehlsdorff TJ, PD Haynes, F Hanke, MC Payne, and NDM Hine. 2016. "Solvent Effects on Electronic Excitations of an Organic Chromophore." <em>Journal of Chemical Theory and</em> <em>Computation</em> 12:1853-1861.</li>
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<li>Zwijnenburg MA, E Berardo, WJ Peveler, and KE Jelfs. 2016. "Amine Molecular Cages as Supramolecular Fluorescent Explosive Sensors: A Computational Perspective." <em>The Journal of Physical Chemistry B</em> 120:5063-5072.</li>
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</ul>
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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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<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 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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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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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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=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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=Ecce Graphical User Interface Provides End-to-End MD Support=
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[[File:Ecce.jpg|left|200px|Ecce’s end-to-end support for molecular dynamics calculations in NWChem greatly increases the ease of use.]]
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[http://ecce.pnl.gov/ Ecce] (Extensible Computational Chemistry Environment) provides full end-to-end support for the molecular dynamics module in NWChem. Through the graphical interface, users can set up their calculations, submit them to their computer platforms, and visualize the results on-the-fly.
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Ecce provides an easy to use graphical user interface that enables novice users to set up quantum chemistry calculations, submit them on large supercomputers, and analyze and visualize the calculated data. The next release will have the capability to build solid state materials and surfaces.
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Latest revision as of 17:52, 22 September 2016

NWChem Related Publications

We highlight NWChem publications from all our users. NWChem related publications are publications detected via a Web-based search that either acknowledge or use NWChem.


2016


  • 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.
  • Adrjan B, W Makulski, K Jackowski, TB Demissie, K Ruud, A Antušek, and M Jaszuński. 2016. "NMR Absolute Shielding Scale and Nuclear Magnetic Dipole Moment of 207Pb." Physical Chemistry Chemical Physics 18:16483-16490.
  • Al-Balushi RA, A Haque, M Jayapal, MK Al-Suti, J Husband, MS Khan, OF Koentjoro, KC Molloy, JM Skelton, and PR Raithby. 2016. "Experimental and Theoretical Investigation for the Level of Conjugation in Carbazole-Based Precursors and Their Mono-, Di-, and Polynuclear Pt(II) Complexes." Inorganic Chemistry 55:6465-6480.
  • 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.
  • Ayed T, J Pilmé, D Tézé, F Bassal, J Barbet, M Chérel, J Champion, R Maurice, G Montavon, and N Galland. 2016. "211At-Labeled Agents for Alpha-Immunotherapy: On the in vivo Stability of Astatine-Agent Bonds." European Journal of Medicinal Chemistry 116:156-164.
  • 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.
  • Brückner C and B Engels. 2016. "A Theoretical Description of Charge Reorganization Energies in Molecular Organic P-Type Semiconductors." Journal of Computational Chemistry 37:1335-1344.
  • 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.
  • Boschen JS, J Lee, TL Windus, JW Evans, and D-J Liu. 2016. "Size Dependence of S-bonding on (111) Facets of Cu Nanoclusters." The Journal of Physical Chemistry C 120:10268-10274.
  • Brabec J, C Yang, E Epifanovsky, AI Krylov, and E Ng. 2016. "Reduced-Cost Sparsity-Exploiting Algorithm for Solving Coupled-Cluster Equations." Journal of Computational Chemistry 37:1059-1067.
  • Bristow JK, KL Svane, D Tiana, JM Skelton, JD Gale, and A Walsh. 2016. "Free Energy of Ligand Removal in the Metal–Organic Framework UiO-66." The Journal of Physical Chemistry C 120:9276-9281.
  • Campo JMd. 2016. "B88 Exchange Functional Recovering the Local Spin Density Linear Response." Theoretical Chemistry Accounts 135: Article no. 179.
  • Carmona-Espíndola J, JL Gázquez, A Vela, and SB Trickey. 2016. "Global Hybrid Exchange Energy Functional with Correct Asymptotic Behavior of the Corresponding Potential." Theoretical Chemistry Accounts 135:Article no. 120.
  • Carrillo J-MY, Z Seibers, R Kumar, MA Matheson, JF Ankner, M Goswami, K Bhaskaran-Nair, WA Shelton, BG Sumpter, and SM Kilbey, II. 2016. "Petascale Simulations of the Morphology and the Molecular Interface of Bulk Heterojunctions." ACS Nano 10:7008-7022.
  • Chen W, G-H Chen, D Wu, and Q Wang. 2016. "BNg3F3: The First Three Noble Gas Atoms Inserted into Mono-Centric Neutral Compounds - a Theoretical Study." Physical Chemistry Chemical Physics 18:17534-17545.
  • 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.
  • Dau PD, D Rios, Y Gong, MC Michelini, J Marçalo, DK Shuh, M Mogannam, MJ Van Stipdonk, TA Corcovilos, JK Martens, G Berden, J Oomens, B Redlich, and JK Gibson. 2016. "Synthesis and Hydrolysis of Uranyl, Neptunyl, and Plutonyl Gas-Phase Complexes Exhibiting Discrete Actinide–Carbon Bonds." Organometallics 35:1228-1240.
  • Douhaya YV, VV Barkaline, and A Tsakalof. 2016. "Computer-Simulation-Based Selection of Optimal Monomer for Imprinting of Tri-O-Acetyl Adenosine in a Polymer Matrix: Calculations for Benzene Solution." Journal of Molecular Modeling 22:Article no. 154.
  • Duanmu K, O Roberto-Neto, FBC Machado, JA Hansen, J Shen, P Piecuch, and DG Truhlar. 2016. "Geometries, Binding Energies, Ionization Potentials, and Electron Affinities of Metal Clusters: Mgn0, ± 1, n = 1–7." The Journal of Physical Chemistry C 120:13275-13286.
  • Duignan TJ and J Autschbach. 2016. "Impact of the Kohn–Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide Complexes." Journal of Chemical Theory and Computation 12:3109-3121.
  • 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.
  • Ermanis K, KEB Parkes, T Agback, and JM Goodman. 2016. "Expanding DP4: Application to Drug Compounds and Automation." Organic & Biomolecular Chemistry 14:3943-3949.
  • Evtimova J, E Drioli, and G De Luca. 2016. "A Density Functional Theory Study of Hydrogen Occupation in VNiTi Alloys Used for Dense Metal Membranes." Journal of Alloys and Compounds 665:225-230.
  • Fang W, J Chen, M Rossi, Y Feng, X-Z Li, and A Michaelides. 2016. "Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs." The Journal of Physical Chemistry Letters 7:2125-2131.
  • 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.
  • Fayon P and A Trewin. 2016. "Formation Mechanism of Ultra Porous Framework Materials." Physical Chemistry Chemical Physics 18:16840-16847.
  • 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.
  • Fischer SA, CJ Cramer, and N Govind. 2016. "Excited-State Absorption from Real-Time Time-Dependent Density Functional Theory: Optical Limiting in Zinc Phthalocyanine." The Journal of Physical Chemistry Letters 7:1387-1391.
  • Fornari RP, J Aragó, and A Troisi. 2016. "Exciton Dynamics in Phthalocyanine Molecular Crystals." The Journal of Physical Chemistry C 120:7987-7996.
  • Fosso-Tande J, T-S Nguyen, G Gidofalvi, and AE DePrince, III. 2016. "Large-Scale Variational Two-Electron Reduced-Density-Matrix-Driven Complete Active Space Self-Consistent Field Methods." Journal of Chemical Theory and Computation 12:2260-2271.
  • Fox SJ, MHUT Fazil, C Dhand, M Venkatesh, ETL Goh, S Harini, C Eugene, RR Lim, S Ramakrishna, SS Chaurasia, RW Beuerman, CS Verma, NK Verma, XJ Loh, and R Lakshminarayanan. 2016. "Insight into Membrane Selectivity of Linear and Branched Polyethylenimines and Their Potential as Biocides for Advanced Wound Dressings." Acta Biomaterialia 37:155-164.
  • Fujii M, W Shin, T Yasuda, and K Yamashita. 2016. "Photon-Absorbing Charge-Bridging States in Organic Bulk Heterojunctions Consisting of Diketopyrrolopyrrole Derivatives and PCBM." Physical Chemistry Chemical Physics 18:9514-9523.
  • Gaines E, K Maisuria, and D Di Tommaso. 2016. "The Role of Solvent in the Self-Assembly of m-Aminobenzoic Acid: A Density Functional Theory and Molecular Dynamics Study." CrystEngComm 18:2937-2948.
  • 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.
  • Ghambarian M, Z Azizi, and M Ghashghaee. 2016. "Diversity of Monomeric Dioxo Chromium Species in Cr/Silicalite-2 Catalysts: A Hybrid Density Functional Study." Computational Materials Science 118:147-154.
  • 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.
  • Göttle AJ, F Alary, M Boggio-Pasqua, IM Dixon, J-L Heully, A Bahreman, SHC Askes, and S Bonnet. 2016. "Pivotal Role of a Pentacoordinate 3MC State on the Photocleavage Efficiency of a Thioether Ligand in Ruthenium(II) Complexes: A Theoretical Mechanistic Study." Inorganic Chemistry 55:4448-4456.
  • Götz DA, A Shayeghi, RL Johnston, P Schwerdtfeger, and R Schäfer. 2016. "Structural Evolution and Metallicity of Lead Clusters." Nanoscale 8:11153-11160.
  • 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.
  • Gunaratne KDD, V Prabhakaran, A Andersen, GE Johnson, and J Laskin. 2016. "Charge Retention of Soft-Landed Phosphotungstate Keggin Anions on Self-Assembled Monolayers." Physical Chemistry Chemical Physics 18:9021-9028.
  • Gupta T and G Rajaraman. 2016. "Modelling Spin Hamiltonian Parameters of Molecular Nanomagnets." Chemical Communications 52:8972-9008.
  • 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.
  • Hermann G, V Pohl, JC Tremblay, B Paulus, H-C Hege, and A Schild. 2016. "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data." Journal of Computational Chemistry 37:1511-1520.
  • Hey JC, LC Smeeton, MT Oakley, and RL Johnston. 2016. "Isomers and Energy Landscapes of Perchlorate–Water Clusters and a Comparison to Pure Water and Sulfate–Water Clusters." The Journal of Physical Chemistry A 120:4008-4015.
  • Hosseini Lavasani SM, H Nejat Pishkenari, and A Meghdari. 2016. "Mechanism of 1,12-Dicarba-closo-dodecaborane Mobility on Gold Substrate as a Nanocar Wheel." The Journal of Physical Chemistry C 120:14048-14058.
  • Hou G-L, M Valiev, and X-B Wang. 2016. "Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications." The Journal of Physical Chemistry A 120:2342-2349.
  • 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.
  • Janocha S, Y Carius, M Hutter, CRD Lancaster, and R Bernhardt. 2016. "Crystal Structure of CYP106A2 in Substrate-Free and Substrate-Bound Form." ChemBioChem 17:852-860.
  • Jia C, A Migliore, N Xin, S Huang, J Wang, Q Yang, S Wang, H Chen, D Wang, B Feng, Z Liu, G Zhang, D-H Qu, H Tian, MA Ratner, HQ Xu, A Nitzan, and X Guo. 2016. "Covalently Bonded Single-Molecule Junctions with Stable and Reversible Photoswitched Conductivity." Science 352:1443-1445.
  • Jindal N, V Lotrich, E Deumens, and BA Sanders. 2016. "Exploiting GPUs with the Super Instruction Architecture." International Journal of Parallel Programming 44:309-324.
  • 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.
  • Kayanuma M, M Shoji, M Yohda, M Odaka, and Y Shigeta. 2016. "Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study." The Journal of Physical Chemistry B 120:3259-3266.Kaydashev V, P Ferrari, C Heard, E Janssens, RL Johnston, and P Lievens. 2016. "Optical Absorption of Small Palladium-Doped Gold Clusters." Particle & Particle Systems Characterization 33:364-372.
  • Kelley MP, P Yang, SB Clark, and AE Clark. 2016. "Structural and Thermodynamic Properties of the CmIII Ion Solvated by Water and Methanol." Inorganic Chemistry 55:4992-4999.Khetrapal NS, T Jian, R Pal, GV Lopez, S Pande, L-S Wang, and XC Zeng. 2016. "Probing the Structures of Gold-Aluminum Alloy Clusters AuxAly-: A Joint Experimental and Theoretical Study." Nanoscale 8:9805-9814.
  • Khrenova MG, ED Kots, AM Kulakova, and IV Polyakov. 2016. "Modeling GTP Hydrolysis in RasGAP Protein Complex." Moscow University Chemistry Bulletin 71:21-24.
  • Khrenova MG, ED Kots, and AV Nemukhin. 2016. "Reaction Mechanism of Guanosine Triphosphate Hydrolysis by the Vision-Related Protein Complex Arl3–RP2." The Journal of Physical Chemistry B 120:3873-3879.
  • Khetrapal NS, T Jian, R Pal, GV Lopez, S Pande, L-S Wang, and XC Zeng. 2016. "Probing the Structures of Gold-Aluminum Alloy Clusters AuxAly-: A Joint Experimental and Theoretical Study." Nanoscale 8:9805-9814.
  • 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.
  • Kobayashi T, FA Perras, TW Goh, TL Metz, W Huang, and M Pruski. 2016. "DNP-Enhanced Ultrawideline Solid-State NMR Spectroscopy: Studies of Platinum in Metal–Organic Frameworks." The Journal of Physical Chemistry Letters 7:2322-2327.
  • 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.
  • Koda S, M Fujii, S Hatamiya, and K Yamashita. 2016. "Dipole Analyses for Short-Circuit Current in Organic Photovoltaic Devices of Diketopyrrolopyrrole-Based Donor and PCBM." Theoretical Chemistry Accounts 135:Article no. 115.Kots ED, MG Khrenova, SV Lushchekina, SD Varfolomeev, BL Grigorenko, and AV Nemukhin. 2016. "Modeling the Complete Catalytic Cycle of Aspartoacylase." The Journal of Physical Chemistry B 120:4221-4231.
  • Kots ED, MG Khrenova, SV Lushchekina, SD Varfolomeev, BL Grigorenko, and AV Nemukhin. 2016. "Modeling the Complete Catalytic Cycle of Aspartoacylase." The Journal of Physical Chemistry B 120:4221-4231.
  • 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.
  • Kratz EG, RE Duke, and GA Cisneros. 2016. "Long-Range Electrostatic Corrections in Multipolar/Polarizable QM/MM Simulations." Theoretical Chemistry Accounts 135:Article no. 166.
  • Kratz EG, AR Walker, L Lagardère, F Lipparini, J-P Piquemal, and GA Cisneros. 2016. "LICHEM: A QM/MM Program for Simulations with Multipolar and Polarizable Force Fields." Journal of Computational Chemistry 37:1019-1029.
  • 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.
  • Kuisma M, A Lundin, K Moth-Poulsen, P Hyldgaard, and P Erhart. 2016. "Optimization of Norbornadiene Compounds for Solar Thermal Storage by First-Principles Calculations." ChemSusChem 9:1786-1794.
  • 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.
  • Li J, G D’Avino, I Duchemin, D Beljonne, and X Blase. 2016. "Combining the Many-Body GW Formalism with Classical Polarizable Models: Insights on the Electronic Structure of Molecular Solids." The Journal of Physical Chemistry Letters 7:2814-2820.
  • Lian S, DJ Weinberg, RD Harris, MS Kodaimati, and EA Weiss. 2016. "Subpicosecond Photoinduced Hole Transfer from a CdS Quantum Dot to a Molecular Acceptor Bound Through an Exciton-Delocalizing Ligand." ACS Nano 10:6372-6382.
  • Liang R, JMJ Swanson, Y Peng, M Wikström, and GA Voth. 2016. "Multiscale Simulations Reveal Key Features of the Proton-Pumping Mechanism in Cytochrome c Oxidase." Proceedings of the National Academy of Sciences 113:7420-7425.
  • Liu X, J Zhang, L Yang, and R Sun. 2016. "Theoretical Studies on F + NH2Cl Reaction: Nucleophilic Substitution at Neutral Nitrogen." The Journal of Physical Chemistry A 120:3740-3746.Li X, X Xu, X You, and DG Truhlar. 2016. "Benchmark Calculations for Bond Dissociation Enthalpies of Unsaturated Methyl Esters and the Bond Dissociation Enthalpies of Methyl Linolenate." The Journal of Physical Chemistry A 120:4025-4036.
  • Lüthi HP, S Heinen, G Schneider, A Glöss, MP Brändle, RA King, E Pyzer-Knapp, FH Alharbi, and S Kais. 2016. "The Quantum Chemical Search for Novel Materials and the Issue of Data Processing: The InfoMol Project." Journal of Computational Science 15:65-73.
  • 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.
  • Makhyoun MA, RA Palmer, AA Soayed, HM Refaat, and DE Basher. 2016. "Synthesis, Crystal Structure and Comparative DFT Studies of a 1D Ni(II) Polymeric Complex of 2-Hydroxypyridine-N-oxide." Journal of Chemical Crystallography 46:269-279.
  • 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.
  • Moon J, TK Kim, and J Kim. 2016. "Ground and Low-Lying Excited States of PtCN and PdCN: Theoretical Investigation Including Spin-Orbit Coupling." Theoretical Chemistry Accounts 135:Article no. 127.
  • 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.
  • Nechay MR, NM Gallup, A Morgenstern, QA Smith, ME Eberhart, and AN Alexandrova. 2016. "Histone Deacetylase 8: Characterization of Physiological Divalent Metal Catalysis." The Journal of Physical Chemistry B 120:5884-5895.
  • Ng CH, CA Ohlin, S Qiu, C Sun, and B Winther-Jensen. 2016. "Mechanistic Studies of the Photo-Electrochemical Hydrogen Evolution Reaction on Poly(2,2′-bithiophene)." Catalysis Science & Technology 6:3253-3262.
  • Pacheco-Kato JC, JM del Campo, JL Gázquez, SB Trickey, and A Vela. 2016. "A PW91-Like Exchange with a Simple Analytical Form." Chemical Physics Letters 651:268-273.
  • 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.
  • Pichugina DA, YG Polynskaya, and NE Kuz'menko. 2016. "Spin and Structural Features of Oxygen Dissociation on Tetrahedral Ag20 and Ag19>Au Clusters." Physical Chemistry Chemical Physics 18:18033-18044.
  • Piekielna J, R De Marco, L Gentilucci, MC Cerlesi, G Calo, C Tömböly, R Artali, and A Janecka. 2016. "Redoubling the Ring Size of an Endomorphin-2 Analog Transforms a Centrally Acting Mu-Opioid Receptor Agonist into a Pure Peripheral Analgesic." Peptide Science 106:309-317.
  • Pliss EM, ME Soloviev, IV Tikhonov, DV Loshadkin, and AL Buchachenko. 2016. "Quantum-Chemical Analysis of the Disproportionation of Nitroxyl and Peroxyl Radicals in Oxidizing Organic Compounds." Russian Journal of Physical Chemistry B 10:417-420.
  • Pruski M, AD Sadow, II Slowing, CL Marshall, P Stair, J Rodriguez, A Harris, GA Somorjai, J Biener, C Matranga, C Wang, JA Schaidle, GT Beckham, DA Ruddy, T Deutsch, SM Alia, C Narula, S Overbury, T Toops, RM Bullock, CHF Peden, Y Wang, MD Allendorf, J Nørskov, and T Bligaard. 2016. "Virtual Special Issue on Catalysis at the U.S. Department of Energy’s National Laboratories." ACS Catalysis 6:3227-3235.
  • Ramharack P and MES Soliman. 2016. "Zika Virus Drug Targets: A Missing Link in Drug Design and Discovery - a Route Map to Fill the Gap." RSC Advances 6:68719-68731.
  • Rakhuba MV and IV Oseledets. 2016. "Grid-Based Electronic Structure Calculations: The Tensor Decomposition Approach." Journal of Computational Physics 312:19-30.
  • Rashev S and DC Moule. 2016. "Theoretical Study on the Vibrational Structure of S0 Thiophosgene from the Origin to Dissociation." Vibrational Spectroscopy 84:118-126.
  • 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.
  • Ross DAW, PA Scattergood, A Babaei, A Pertegás, HJ Bolink, and PIP Elliott. 2016. "Luminescent Osmium(II) Bi-1,2,3-Triazol-4-yl Complexes: Photophysical Characterisation and Application in Light-Emitting Electrochemical Cells." Dalton Transactions 45:7748-7757.
  • Salter-Blanc AJ, EJ Bylaska, MA Lyon, SC Ness, and PG Tratnyek. 2016. "Structure–Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide." Environmental Science & Technology 50:5094-5102.
  • Sancho-García JC, M Moral, and AJ Pérez-Jiménez. 2016. "Effect of Cyclic Topology on Charge-Transfer Properties of Organic Molecular Semiconductors: The Case of Cycloparaphenylene Molecules." The Journal of Physical Chemistry C 120:9104-9111.
  • 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.
  • Scalambra F, M Serrano-Ruiz, S Nahim-Granados, and A Romerosa. 2016. "Ruthenium Complexes Containing 2,2′-Bipyridine and 1,3,5-Triaza-7-phosphaadamantane." European Journal of Inorganic Chemistry 2016:1528-1540.
  • Schrauben JN, A Akdag, J Wen, Z Havlas, JL Ryerson, MB Smith, J Michl, and JC Johnson. 2016. "Excitation Localization/Delocalization Isomerism in a Strongly Coupled Covalent Dimer of 1,3-Diphenylisobenzofuran." The Journal of Physical Chemistry A 120:3473-3483.
  • Shoji M, H Isobe, J-R Shen, and K Yamaguchi. 2016. "Geometric and Electronic Structures of the Synthetic Mn4CaO4 Model Compound Mimicking the Photosynthetic Oxygen-Evolving Complex." Physical Chemistry Chemical Physics 18:11330-11340.Sergentu D-C, G David, G Montavon, R Maurice, and N Galland. 2016. "Scrutinizing “Invisible” Astatine: A Challenge for Modern Density Functionals." Journal of Computational Chemistry 37:1345-1354.
  • 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.
  • Simm GN and M Reiher. 2016. "Systematic Error Estimation for Chemical Reaction Energies." Journal of Chemical Theory and Computation 12:2762-2773.
  • 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.
  • South C, G Schoendorff, and AK Wilson. 2016. "Dissociation Energy and Electronic Structure of the Low Valent Lanthanide Compound NdF+." International Journal of Quantum Chemistry 116:791-794.
  • 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.
  • Su NQ and X Xu. 2016. "Second-Order Perturbation Theory for Fractional Occupation Systems: Applications to Ionization Potential and Electron Affinity Calculations." Journal of Chemical Theory and Computation 12:2285-2297.
  • 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.
  • TalwelkarShimpi M, S Öberg, L Giri, and VR Pedireddi. 2016. "Experimental and Theoretical Studies of Molecular Complexes of Theophylline with Some Phenylboronic Acids." RSC Advances 6:43060-43068.
  • 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.
  • Tran VT and QT Tran. 2016. "Quantum Chemical Study of the Low-Lying Electronic States of VSi3–/0 Clusters and Interpretation of the Anion Photoelectron Spectrum." The Journal of Physical Chemistry A 120:5950-5957.
  • Thorley KJ and C Risko. 2016. "Mapping the Configuration Dependence of Electronic Coupling in Organic Semiconductors." Journal of Materials Chemistry C 4:3825-3832.
  • Umadevi P and L Senthilkumar. 2016. "Metal-Interacted Histidine Dimer: An ETS-NOCV and XANES Study." RSC Advances 6:38919-38930.
  • 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 SCNWater 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.
  • Wagner J, P Deglmann, S Fuchs, M Ciesielski, CA Fleckenstein, and M Döring. 2016. "A Flame Retardant Synergism of Organic Disulfides and Phosphorous Compounds." Polymer Degradation and Stability 129:63-76.
  • 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.
  • Woolfson RJ, GA Timco, A Chiesa, IJ Vitorica-Yrezabal, F Tuna, T Guidi, E Pavarini, P Santini, S Carretta, and REP Winpenny. 2016. "[CrF(O2CtBu)2]9: Synthesis and Characterization of a Regular Homometallic Ring with an Odd Number of Metal Centers and Electrons." Angewandte Chemie International Edition 55:8856-8859.
  • Yang Y, Q Wang, W Qiu, H Guo, and F Gao. 2016. "Covalent Immobilization of Cu3(btc)2 at Chitosan–Electroreduced Graphene Oxide Hybrid Film and Its Application for Simultaneous Detection of Dihydroxybenzene Isomers." The Journal of Physical Chemistry C 120:9794-9803.
  • Yao H, Q Dai, and Z You. 2016. "Molecular Dynamics Simulation of Physicochemical Properties of the Asphalt Model." Fuel 164:83-93.
  • Yan W, A Ramanathan, PD Patel, SK Maiti, BB Laird, WH Thompson, and B Subramaniam. 2016. "Mechanistic Insights for Enhancing Activity and Stability of Nb-Incorporated Silicates for Selective Ethylene Epoxidation." Journal of Catalysis 336:75-84.
  • 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 R, Q He, Y Huang, and X Wang. 2016. "Spectroscopic and QM/MM Investigations of Chloroperoxidase Catalyzed Degradation of Orange G." Archives of Biochemistry and Biophysics 596:1-9.
  • 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.
  • Zhang J, L Yang, and L Sheng. 2016. "Electronic Structure Theory Study of the Microsolvated F(H2O) + CH3I SN2 Reaction." The Journal of Physical Chemistry A 120:3613-3622.
  • 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.
  • Zuehlsdorff TJ, PD Haynes, F Hanke, MC Payne, and NDM Hine. 2016. "Solvent Effects on Electronic Excitations of an Organic Chromophore." Journal of Chemical Theory and Computation 12:1853-1861.
  • Zwijnenburg MA, E Berardo, WJ Peveler, and KE Jelfs. 2016. "Amine Molecular Cages as Supramolecular Fluorescent Explosive Sensors: A Computational Perspective." The Journal of Physical Chemistry B 120:5063-5072.


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