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  Subjects -> CHEMISTRY (Total: 849 journals)
    - ANALYTICAL CHEMISTRY (50 journals)
    - CHEMISTRY (598 journals)
    - CRYSTALLOGRAPHY (22 journals)
    - ELECTROCHEMISTRY (25 journals)
    - INORGANIC CHEMISTRY (42 journals)
    - ORGANIC CHEMISTRY (45 journals)
    - PHYSICAL CHEMISTRY (67 journals)

CHEMISTRY (598 journals)                  1 2 3 | Last

Showing 1 - 200 of 735 Journals sorted alphabetically
2D Materials     Hybrid Journal   (Followers: 8)
Accreditation and Quality Assurance: Journal for Quality, Comparability and Reliability in Chemical Measurement     Hybrid Journal   (Followers: 26)
ACS Catalysis     Full-text available via subscription   (Followers: 32)
ACS Chemical Neuroscience     Full-text available via subscription   (Followers: 17)
ACS Combinatorial Science     Full-text available via subscription   (Followers: 23)
ACS Macro Letters     Full-text available via subscription   (Followers: 23)
ACS Medicinal Chemistry Letters     Full-text available via subscription   (Followers: 39)
ACS Nano     Full-text available via subscription   (Followers: 227)
ACS Photonics     Full-text available via subscription   (Followers: 11)
ACS Synthetic Biology     Full-text available via subscription   (Followers: 21)
Acta Chemica Iasi     Open Access   (Followers: 2)
Acta Chimica Sinica     Full-text available via subscription   (Followers: 1)
Acta Chimica Slovaca     Open Access   (Followers: 1)
Acta Chromatographica     Full-text available via subscription   (Followers: 9)
Acta Facultatis Medicae Naissensis     Open Access  
Acta Metallurgica Sinica (English Letters)     Hybrid Journal   (Followers: 5)
Acta Scientifica Naturalis     Open Access   (Followers: 2)
adhäsion KLEBEN & DICHTEN     Hybrid Journal   (Followers: 5)
Adhesion Adhesives & Sealants     Hybrid Journal   (Followers: 7)
Adsorption Science & Technology     Full-text available via subscription   (Followers: 5)
Advanced Functional Materials     Hybrid Journal   (Followers: 50)
Advanced Science Focus     Free   (Followers: 3)
Advances in Chemical Engineering and Science     Open Access   (Followers: 53)
Advances in Chemical Science     Open Access   (Followers: 13)
Advances in Chemistry     Open Access   (Followers: 14)
Advances in Colloid and Interface Science     Full-text available via subscription   (Followers: 18)
Advances in Drug Research     Full-text available via subscription   (Followers: 22)
Advances in Enzyme Research     Open Access   (Followers: 9)
Advances in Fluorine Science     Full-text available via subscription   (Followers: 8)
Advances in Fuel Cells     Full-text available via subscription   (Followers: 15)
Advances in Heterocyclic Chemistry     Full-text available via subscription   (Followers: 8)
Advances in Materials Physics and Chemistry     Open Access   (Followers: 19)
Advances in Nanoparticles     Open Access   (Followers: 14)
Advances in Organometallic Chemistry     Full-text available via subscription   (Followers: 15)
Advances in Polymer Science     Hybrid Journal   (Followers: 41)
Advances in Protein Chemistry     Full-text available via subscription   (Followers: 18)
Advances in Protein Chemistry and Structural Biology     Full-text available via subscription   (Followers: 19)
Advances in Quantum Chemistry     Full-text available via subscription   (Followers: 5)
Advances in Science and Technology     Full-text available via subscription   (Followers: 12)
African Journal of Bacteriology Research     Open Access  
African Journal of Chemical Education     Open Access   (Followers: 2)
African Journal of Pure and Applied Chemistry     Open Access   (Followers: 7)
Agrokémia és Talajtan     Full-text available via subscription   (Followers: 2)
Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (Followers: 3)
AMB Express     Open Access   (Followers: 1)
Ambix     Hybrid Journal   (Followers: 3)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 67)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 14)
American Journal of Chemistry     Open Access   (Followers: 26)
American Journal of Plant Physiology     Open Access   (Followers: 13)
American Mineralogist     Hybrid Journal   (Followers: 13)
Analyst     Full-text available via subscription   (Followers: 38)
Angewandte Chemie     Hybrid Journal   (Followers: 158)
Angewandte Chemie International Edition     Hybrid Journal   (Followers: 208)
Annales UMCS, Chemia     Open Access   (Followers: 1)
Annals of Clinical Chemistry and Laboratory Medicine     Open Access   (Followers: 1)
Annual Reports in Computational Chemistry     Full-text available via subscription   (Followers: 3)
Annual Reports Section A (Inorganic Chemistry)     Full-text available via subscription   (Followers: 3)
Annual Reports Section B (Organic Chemistry)     Full-text available via subscription   (Followers: 8)
Annual Review of Chemical and Biomolecular Engineering     Full-text available via subscription   (Followers: 12)
Annual Review of Food Science and Technology     Full-text available via subscription   (Followers: 14)
Anti-Infective Agents     Hybrid Journal   (Followers: 3)
Antiviral Chemistry and Chemotherapy     Hybrid Journal  
Applied Organometallic Chemistry     Hybrid Journal   (Followers: 7)
Applied Spectroscopy     Full-text available via subscription   (Followers: 23)
Applied Surface Science     Hybrid Journal   (Followers: 28)
Arabian Journal of Chemistry     Open Access   (Followers: 6)
ARKIVOC     Open Access   (Followers: 2)
Asian Journal of Biochemistry     Open Access   (Followers: 1)
Atomization and Sprays     Full-text available via subscription   (Followers: 3)
Australian Journal of Chemistry     Hybrid Journal   (Followers: 7)
Autophagy     Hybrid Journal   (Followers: 2)
Avances en Quimica     Open Access   (Followers: 1)
Biochemical Pharmacology     Hybrid Journal   (Followers: 10)
Biochemistry     Full-text available via subscription   (Followers: 283)
Biochemistry Insights     Open Access   (Followers: 5)
Biochemistry Research International     Open Access   (Followers: 6)
BioChip Journal     Hybrid Journal  
Bioinorganic Chemistry and Applications     Open Access   (Followers: 9)
Bioinspired Materials     Open Access   (Followers: 5)
Biointerface Research in Applied Chemistry     Open Access   (Followers: 2)
Biointerphases     Open Access   (Followers: 1)
Biology, Medicine, & Natural Product Chemistry     Open Access   (Followers: 1)
Biomacromolecules     Full-text available via subscription   (Followers: 19)
Biomass Conversion and Biorefinery     Partially Free   (Followers: 10)
Biomedical Chromatography     Hybrid Journal   (Followers: 6)
Biomolecular NMR Assignments     Hybrid Journal   (Followers: 3)
BioNanoScience     Partially Free   (Followers: 4)
Bioorganic & Medicinal Chemistry     Hybrid Journal   (Followers: 108)
Bioorganic & Medicinal Chemistry Letters     Hybrid Journal   (Followers: 93)
Bioorganic Chemistry     Hybrid Journal   (Followers: 10)
Biopolymers     Hybrid Journal   (Followers: 18)
Biosensors     Open Access   (Followers: 2)
Biotechnic and Histochemistry     Hybrid Journal   (Followers: 1)
Bitácora Digital     Open Access  
Boletin de la Sociedad Chilena de Quimica     Open Access  
Bulletin of the Chemical Society of Ethiopia     Open Access   (Followers: 2)
Bulletin of the Chemical Society of Japan     Full-text available via subscription   (Followers: 24)
Bulletin of the Korean Chemical Society     Hybrid Journal   (Followers: 1)
C - Journal of Carbon Research     Open Access   (Followers: 3)
Cakra Kimia (Indonesian E-Journal of Applied Chemistry)     Open Access  
Canadian Association of Radiologists Journal     Full-text available via subscription   (Followers: 2)
Canadian Journal of Chemistry     Hybrid Journal   (Followers: 10)
Canadian Mineralogist     Full-text available via subscription   (Followers: 3)
Carbohydrate Research     Hybrid Journal   (Followers: 26)
Carbon     Hybrid Journal   (Followers: 67)
Catalysis for Sustainable Energy     Open Access   (Followers: 6)
Catalysis Reviews: Science and Engineering     Hybrid Journal   (Followers: 8)
Catalysis Science and Technology     Free   (Followers: 6)
Catalysis Surveys from Asia     Hybrid Journal   (Followers: 3)
Catalysts     Open Access   (Followers: 7)
Cellulose     Hybrid Journal   (Followers: 7)
Cereal Chemistry     Full-text available via subscription   (Followers: 4)
ChemBioEng Reviews     Full-text available via subscription   (Followers: 1)
ChemCatChem     Hybrid Journal   (Followers: 8)
Chemical and Engineering News     Free   (Followers: 12)
Chemical Bulletin of Kazakh National University     Open Access  
Chemical Communications     Full-text available via subscription   (Followers: 70)
Chemical Engineering Research and Design     Hybrid Journal   (Followers: 23)
Chemical Research in Chinese Universities     Hybrid Journal   (Followers: 3)
Chemical Research in Toxicology     Full-text available via subscription   (Followers: 19)
Chemical Reviews     Full-text available via subscription   (Followers: 170)
Chemical Science     Open Access   (Followers: 21)
Chemical Technology     Open Access   (Followers: 16)
Chemical Vapor Deposition     Hybrid Journal   (Followers: 5)
Chemical Week     Full-text available via subscription   (Followers: 8)
Chemie in Unserer Zeit     Hybrid Journal   (Followers: 55)
Chemie-Ingenieur-Technik (Cit)     Hybrid Journal   (Followers: 25)
ChemInform     Hybrid Journal   (Followers: 8)
Chemistry & Biodiversity     Hybrid Journal   (Followers: 6)
Chemistry & Biology     Full-text available via subscription   (Followers: 30)
Chemistry & Industry     Hybrid Journal   (Followers: 5)
Chemistry - A European Journal     Hybrid Journal   (Followers: 144)
Chemistry - An Asian Journal     Hybrid Journal   (Followers: 15)
Chemistry and Materials Research     Open Access   (Followers: 18)
Chemistry Central Journal     Open Access   (Followers: 4)
Chemistry Education Research and Practice     Free   (Followers: 5)
Chemistry in Education     Open Access   (Followers: 9)
Chemistry International     Hybrid Journal   (Followers: 2)
Chemistry Letters     Full-text available via subscription   (Followers: 45)
Chemistry of Materials     Full-text available via subscription   (Followers: 226)
Chemistry of Natural Compounds     Hybrid Journal   (Followers: 9)
Chemistry World     Full-text available via subscription   (Followers: 22)
Chemistry-Didactics-Ecology-Metrology     Open Access  
ChemistryOpen     Open Access   (Followers: 2)
Chemkon - Chemie Konkret, Forum Fuer Unterricht Und Didaktik     Hybrid Journal  
Chemoecology     Hybrid Journal   (Followers: 2)
Chemometrics and Intelligent Laboratory Systems     Hybrid Journal   (Followers: 15)
Chemosensors     Open Access  
ChemPhysChem     Hybrid Journal   (Followers: 9)
ChemPlusChem     Hybrid Journal   (Followers: 2)
ChemTexts     Hybrid Journal  
CHIMIA International Journal for Chemistry     Full-text available via subscription   (Followers: 2)
Chinese Journal of Chemistry     Hybrid Journal   (Followers: 6)
Chinese Journal of Polymer Science     Hybrid Journal   (Followers: 10)
Chromatographia     Hybrid Journal   (Followers: 24)
Chromatography Research International     Open Access   (Followers: 7)
Clay Minerals     Full-text available via subscription   (Followers: 9)
Cogent Chemistry     Open Access  
Colloid and Interface Science Communications     Open Access  
Colloid and Polymer Science     Hybrid Journal   (Followers: 10)
Colloids and Surfaces B: Biointerfaces     Hybrid Journal   (Followers: 8)
Combinatorial Chemistry & High Throughput Screening     Hybrid Journal   (Followers: 3)
Combustion Science and Technology     Hybrid Journal   (Followers: 18)
Comments on Inorganic Chemistry: A Journal of Critical Discussion of the Current Literature     Hybrid Journal   (Followers: 2)
Composite Interfaces     Hybrid Journal   (Followers: 6)
Comprehensive Chemical Kinetics     Full-text available via subscription   (Followers: 2)
Comptes Rendus Chimie     Full-text available via subscription  
Comptes Rendus Physique     Full-text available via subscription   (Followers: 1)
Computational and Theoretical Chemistry     Hybrid Journal   (Followers: 9)
Computational Biology and Chemistry     Hybrid Journal   (Followers: 12)
Computational Chemistry     Open Access   (Followers: 2)
Computers & Chemical Engineering     Hybrid Journal   (Followers: 9)
Coordination Chemistry Reviews     Full-text available via subscription   (Followers: 2)
Copernican Letters     Open Access  
Critical Reviews in Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 5)
Crystal Structure Theory and Applications     Open Access   (Followers: 3)
CrystEngComm     Full-text available via subscription   (Followers: 11)
Current Catalysis     Hybrid Journal   (Followers: 2)
Current Metabolomics     Hybrid Journal   (Followers: 5)
Current Opinion in Colloid & Interface Science     Hybrid Journal   (Followers: 9)
Current Research in Chemistry     Open Access   (Followers: 8)
Current Science     Open Access   (Followers: 56)
Dalton Transactions     Full-text available via subscription   (Followers: 20)
Detection     Open Access   (Followers: 2)
Developments in Geochemistry     Full-text available via subscription   (Followers: 2)
Diamond and Related Materials     Hybrid Journal   (Followers: 12)
Dislocations in Solids     Full-text available via subscription  
Doklady Chemistry     Hybrid Journal  
Drying Technology: An International Journal     Hybrid Journal   (Followers: 4)
Eclética Química     Open Access   (Followers: 1)
Ecological Chemistry and Engineering S     Open Access   (Followers: 4)
Ecotoxicology and Environmental Contamination     Open Access  
Educación Química     Open Access   (Followers: 1)
Education for Chemical Engineers     Hybrid Journal   (Followers: 5)
EJNMMI Radiopharmacy and Chemistry     Open Access  
Elements     Full-text available via subscription   (Followers: 2)
Environmental Chemistry     Hybrid Journal   (Followers: 9)
Environmental Chemistry Letters     Hybrid Journal   (Followers: 4)
Environmental Science & Technology Letters     Full-text available via subscription   (Followers: 5)

        1 2 3 | Last

Journal Cover Annual Reports in Computational Chemistry
  [SJR: 0.954]   [H-I: 18]   [3 followers]  Follow
    
   Full-text available via subscription Subscription journal
   ISSN (Print) 1574-1400
   Published by Elsevier Homepage  [3042 journals]
  • Annual Reports in Computational Chemistry
    • Abstract: Publication date: 2016
      Source:Annual Reports in Computational Chemistry, Volume 12


      PubDate: 2016-10-10T16:35:50Z
       
  • Cumulative Index
    • Abstract: Publication date: 2016
      Source:Annual Reports in Computational Chemistry, Volume 12


      PubDate: 2016-10-10T16:35:50Z
       
  • Computer Simulation and Modeling Techniques in the Study of
           Nanoparticle-Membrane Interactions
    • Authors: Wang
      Abstract: Publication date: Available online 3 June 2016
      Source:Annual Reports in Computational Chemistry
      Author(s): Z. Ge, Y. Wang
      Given the increased exposure of our environment to nanoparticles (NPs), extensive research has been performed to investigate their interactions with biological systems with the hope of developing NPs that are both safer and more efficient in their designed functions. The plasma membrane represents the first barrier against the entry of nanoparticles into a cell. Depending on their physicochemical properties, most NPs either undergo direct translocation or use the endocytosis pathway to cross this barrier. In this chapter, we review recent computational studies aimed at understanding NP-membrane interactions during these processes. The focus is the technical aspects of these studies to provide a detailed account of the simulation and modeling approaches, which range from all-atom to coarse-grained molecular dynamics simulations, dissipative particle dynamics simulations to continuum modeling. We highlight key steps in the construction and parameterization of the NP model under the framework of each method, followed by example applications reported in recent years. In the last section, we briefly discuss the prospect and challenges of computer simulation and modeling studies aimed at understanding NP-membrane interactions.

      PubDate: 2016-06-15T15:22:20Z
       
  • Prediction of Thermochemical Properties Across the Periodic Table: A
           Review of the correlation consistent Composite Approach (ccCA) Strategies
           and Applications
    • Authors: Peterson D.A.; Penchoff A.K. Wilson
      Abstract: Publication date: Available online 5 May 2016
      Source:Annual Reports in Computational Chemistry
      Author(s): C. Peterson, D.A. Penchoff, A.K. Wilson
      Accurate predictions of thermochemical and spectroscopic properties present challenges as computational costs (eg, memory, disk space, and CPU time) increase when the size of the molecular species and basis sets increase. The correlation consistent Composite Approach (ccCA) is an ab initio composite method that has been designed without empirically optimized parameters to model the energetics of molecules with a goal of predicting energetics within 1kcal/mol for main group species, 3kcal/mol for transition metal species, and 5kcal/mol for lanthanides, from reliable, well-established experimental values. ccCA combines a series of less computationally expensive, albeit, less accurate methodologies, to replicate a much more costly, though much more accurate methodology. Variants of ccCA have been developed to predict chemical properties of compounds containing elements throughout the periodic table. These ccCA variants include methods to accurately describe transition metals, as well as heavy main group, and f-block elements. Some ccCA formulations have been designed to enable the description of large complexes and biomolecules, as well as incorporating solvation effects. An overview of ccCA, the different variants of the method, and applications to organic, transition metal, biochemical, and heavy element species are discussed.

      PubDate: 2016-05-05T19:31:03Z
       
  • Recoupled Pair Bonding: Unifying the Theory of Valence for the Main Group
           Elements
    • Authors: T.H. Dunning; D.E. Woon L.T. T.Y. Takeshita B.A. Lindquist Leiding
      Abstract: Publication date: Available online 23 March 2016
      Source:Annual Reports in Computational Chemistry
      Author(s): T.H. Dunning, D.E. Woon, L.T. Xu, T.Y. Takeshita, B.A. Lindquist, J. Leiding
      The valence of an element often exceeds the number of singly occupied orbitals in the electronic configuration of the ground state of the atom. In the early main group elements, the increase in valence is attributed to the formation of sp n hybrid orbitals and in the late main group elements beyond the first row to the formation of 3-center, 4-electron (3c-4e) bonds. Our studies have shown that a single new concept—recoupled pair bonding—underlies the increases in valence in both groups of elements. In this report, we describe recent studies of the CF n and SF n molecules that illustrate the nature of recoupled pair bonds and recoupled pair bond dyads and compare and contrast the recoupled pair bonds formed with the electrons in ns lone pairs (early main group elements) and np lone pairs (late main group elements beyond the first row). Recoupled pair bonding also accounts for many of the other differences in the chemistry of the elements in the first and subsequent rows of the Periodic Table, which is known as the first row anomaly.

      PubDate: 2016-03-26T02:30:36Z
       
  • The Impact of Larger Basis Sets and Explicitly Correlated Coupled Cluster
           Theory on the Feller–Peterson–Dixon Composite Method
    • Authors: D. Feller; K.A. Peterson; D.A. Dixon
      Pages: 47 - 78
      Abstract: Publication date: Available online 8 August 2016
      Source:Annual Reports in Computational Chemistry
      Author(s): D. Feller, K.A. Peterson, D.A. Dixon
      The degree of completeness in the one-particle expansion, which in most standard orbital–based electronic structure methods involves atom-centered Gaussian basis functions, is central to the prediction of accurate atomic and molecular properties. While there are hundreds of basis sets in the literature capable of yielding low-to-medium quality results, high accuracy requires the use of a convergent and computationally efficient sequence of basis sets capable of systematically addressing the painfully slow one-particle expansion. This issue will be discussed in the context of the Feller–Peterson–Dixon composite method which is intended for well-converged thermochemical and spectroscopic properties across a large portion of the periodic table. Two strategies, one involving very large basis sets and the other involving newly developed, explicitly correlated methods, will be contrasted. Comparison with well-established experimental data covering hundreds of chemical systems (neutral molecules, anions, and cations in both ground and excited states) demonstrates that this admittedly computationally expensive approach is capable of achieving root–mean–square deviation agreement for atomization energies, electron affinities, and ionization potentials within ±0.5kcal/mol and maximum errors within ±1kcal/mol.

      PubDate: 2016-08-09T02:58:57Z
      DOI: 10.1016/bs.arcc.2016.02.001
       
  • Computational Isotope Geochemistry
    • Authors: J.R. Rustad
      Pages: 117 - 156
      Abstract: Publication date: Available online 8 September 2016
      Source:Annual Reports in Computational Chemistry
      Author(s): J.R. Rustad
      Isotope fractionation factors play a key role in modern geochemistry and are used to interpret a broad range of natural phenomena over a wide range of temporal scales. Experimental advances in this area have been driven by significant improvements in mass spectrometry techniques coupled to advances in computational chemistry methods due to advances in software and substantial improvements in hardware. The prediction of isotope fractionation factors requires the ability to predict harmonic frequencies to high accuracy due to the fact that the changes are often in parts per 1000 (per mil). This requires the choice of a good model system that captures the critical geochemical features, the appropriate choice of the computational electronic structure method (correlated molecular orbital theory at least at the second-order Møller–Plesset theory level vs. density functional theory with an appropriate exchange-correlation functional), the choice of the basis set, and the potential use of implicit models for solvation and/or the solid state environment. This chapter describes the computational approaches needed for the prediction of isotope fractionation factors and provides example of the application of these methods to geochemical systems containing atoms from across the periodic table.

      PubDate: 2016-09-14T01:18:25Z
      DOI: 10.1016/bs.arcc.2016.07.001
       
  • Annual Reports in Computational Chemistry
    • Abstract: Publication date: 2015
      Source:Annual Reports in Computational Chemistry, Volume 11


      PubDate: 2015-12-02T11:53:06Z
       
  • Cumulative Index
    • Abstract: Publication date: 2015
      Source:Annual Reports in Computational Chemistry, Volume 11


      PubDate: 2015-12-02T11:53:06Z
       
  • Intermolecular Network Theory: A General Approach for Understanding the
           Structural and Dynamic Properties of Liquids and Solutions
    • Authors: Aurora Clark
      Abstract: Publication date: Available online 3 November 2015
      Source:Annual Reports in Computational Chemistry
      Author(s): Aurora E. Clark
      Graph theory applications within the physical sciences have a long history. However, it has never moved to the forefront of analytical techniques employed by the computational chemistry community. Though much of the earliest work leveraged percolation theory as a backdrop for understanding critical phenomena and phase transitions within statistical mechanical simulations, modern data science has much to contribute. Here, we focus on the realm of intermolecular networks, where vertices represent molecules or particles, and an edge represents an intermolecular or interparticle interaction. These interactions are widely understood to dictate many of the physical properties of soft matter, and for liquids in particular, understanding this network is essential. Consider the sheer volume of ∼70years of literature associated with the hydrogen bond network of water, a topic that remains an active area of research even today. The aim of this work is twofold: first, to put into context prior algorithms and analyses that employed “connectedness theory” or lattice-based models to understand the intermolecular networks of chemical systems; and second to discuss a more general strategy for analyzing the multiscale structural and dynamic properties of chemical systems—intermolecular network theory. This approach encompasses foundational methods such as percolation theory, but also utilizes contemporary graph theoretical analyses that have evolved alongside the development of the World Wide Web, cloud computing, and big data. It is the realm of intermolecular network theory to determine the relationships between the essential physics of a system and the topological properties of the network and to derive new techniques in graph theory that can be related to the underlying physico-chemical or reactive properties of a system. Examples are used throughout this chapter that demonstrate applications to a wide variety of complex chemical systems, including ion association within electrolytes, mass transport and the properties of liquid–liquid phase boundaries, and multicomponent solutions.

      PubDate: 2015-11-06T19:02:14Z
       
  • The Nonlocal Correlation Density Functional VV10: A Successful Attempt to
           Accurately Capture Noncovalent Interactions
    • Authors: Calbo Enrique; Juan Juan
      Abstract: Publication date: Available online 3 November 2015
      Source:Annual Reports in Computational Chemistry
      Author(s): Joaquín Calbo, Enrique Ortí, Juan C. Sancho-García, Juan Aragó
      In this chapter, we review the most relevant attempts to merge the Vydrov and van Voorhis nonlocal density-dependent functional kernel (VV10) with modern density functionals to accurately describe van der Waals interactions with a reasonable computational cost. The chapter is organized by providing first an introduction of the relevance of van der Waals interactions and the difficulties of common density functionals to describe these forces. Second, the historical developments that eventually give rise to the most modern formulation of the nonlocal density functional VV10 are briefly addressed. Then, an overview of its technical formulation, adjustable parameters, and implementation considerations is given, complemented with recent high-throughput benchmark studies of this approximation, necessarily on dispersion-dominated training databases, which are carefully analyzed to highlight its accuracy versus computational trade-offs. We then guide the reader through the behavior of different rungs of density functionals when they are systematically coupled to the nonlocal VV10 term. A detailed overlook of the most important applications in which the VV10 functional has been applied is undertaken. Finally, a “roadmap” for future improvements of the VV10-type nonlocal approach is presented.

      PubDate: 2015-11-06T19:02:14Z
       
  • NMR Calculations for Paramagnetic Molecules and Metal Complexes
    • Authors: Jochen Autschbach
      Pages: 3 - 36
      Abstract: Publication date: Available online 12 November 2015
      Source:Annual Reports in Computational Chemistry
      Author(s): Jochen Autschbach
      Molecules and metal complexes with paramagnetic ground states or low-energy paramagnetic electronic excited states may exhibit profound effects due to electron paramagnetism on NMR parameters such as nuclear magnetic shielding constants and indirect nuclear spin–spin coupling. This review discusses different approaches that can be used to calculate such effects from first principles, either with or without employing fictitious spin Hamiltonian parameters. Case studies are presented, along with an overview of selected recently published computational studies of NMR chemical shifts of paramagnetic systems.

      PubDate: 2015-11-14T01:13:34Z
      DOI: 10.1016/bs.arcc.2015.09.006
       
  • Modeling Laser-Induced Molecule Excitations Using Real-Time,
           Time-Dependent Density Functional Theory
    • Authors: Attila Bende
      Pages: 103 - 146
      Abstract: Publication date: Available online 11 November 2015
      Source:Annual Reports in Computational Chemistry
      Author(s): Attila Bende
      Real-time, time-dependent density functional theory (RT-TDDFT) treatments of molecule–laser interactions and excited electron population dynamics are reviewed and discussed. After the introductory section, the theoretical background together with different numerical solutions used for the efficient propagation of the electron density in real time is presented. This is followed by a discussion of several real-case applications, including computing the full electronic absorption spectrum, resonant- and charge-transfer-type excitations, and the dynamics of different orbital populations in real time. The roles of the different laser field parameters are emphasized: direction, strength, wavelength, or pulse shape needed in order to get efficient and selective excitation behaviors for a specific molecular system. Some remarks about the advantage and disadvantage of RT-TDDFT as well as about the possible further developments are given at the end of the chapter.

      PubDate: 2015-11-14T01:13:34Z
      DOI: 10.1016/bs.arcc.2015.09.001
       
  • Chemical Bonding, Reactivity, and Viability of Large Boron Clusters
    • Authors: Jules Tshishimbi Muya; Minh Tho Nguyen; Arnout Ceulemans
      Pages: 147 - 187
      Abstract: Publication date: Available online 12 November 2015
      Source:Annual Reports in Computational Chemistry
      Author(s): Jules Tshishimbi Muya, Minh Tho Nguyen, Arnout Ceulemans
      Quantum chemical methods were employed to investigate the structure, bonding, properties, and viability of new inorganic fullerenes based on boron, with the archetypal boron buckyball B80. Two current approaches on large boron nanoclusters include the search for hollow and multiple shells cages. Large boron clusters have only been identified in silico. In this Chapter, we analyze the chemical bonding phenomenon of B80, the symmetry of both B80 and B 80 + , the reactivity of B80 toward nucleophilic or electrophilic reactants, and the aromaticity and the topological indices of viable boron fullerenes. The boron buckyball B80 is isoelectronic with the Buckminsterfullerene C60 and can react as an amphoteric species with both acids (e.g., BH3, AlH3) and bases (e.g., NH3, PH3, N2H4). Both Ih-B80 and B 80 + are unstable, and undergo a symmetry breaking via both pseudo-Jahn–Teller and Jahn–Teller effects. The ring current analysis shows that B80 can conduct current better than C60 and is slightly paramagnetic. A detailed analysis on chemical bonding in a large set of boron fullerenes with partially and totally capped pentagons points out the following key factors that are stabilizing boron buckyballs: omnicapping of pentagons, homogeneous distribution of caps, formation of B10 motifs preferably fused to B16, isolation of empty hexagons and caps, and incorporation of patches of 2D boron sheets.

      PubDate: 2015-11-14T01:13:34Z
      DOI: 10.1016/bs.arcc.2015.09.004
       
  • A Computational Perspective on Multichannel Scattering Theory with
           Applications to Physical and Nuclear Chemistry
    • Authors: Simone Taioli; Stefano Simonucci
      Pages: 191 - 310
      Abstract: Publication date: Available online 10 November 2015
      Source:Annual Reports in Computational Chemistry
      Author(s): Simone Taioli, Stefano Simonucci
      In this chapter we discuss a general theoretical framework, based on the generalization of Fano's approach to discrete–continuum interaction, able to describe a variety of resonant phenomena and decay events, ranging from core-electron spectroscopies to the description of universal properties in ultracold Fermi gases, and from the investigation of β-decay in heavy nuclei to the nucleosynthesis of the elements in stars. This method is capable of analyzing the dynamics of atoms, molecules, and solids under the influence of incident radiation or electronic beams and, simultaneously, to predict quantitatively the spectral line shapes correlating their features with the internal dynamic of the perturbed system. On the computational side, we demonstrate by using the concept of the multichannel scattering T-matrix that our approach is amenable to efficient program implementations for determining numerically continuum wave functions including the main correlation effects. For each application we present a detailed description of the main algorithms and computational procedures used to implement our scattering approach and to limit the computational cost of the calculations.

      PubDate: 2015-11-14T01:13:34Z
      DOI: 10.1016/bs.arcc.2015.09.005
       
  • Chapter One Quantum Chemistry Methods with Multiwavelet Bases on Massive
           Parallel Computers
    • Authors: Álvaro Vázquez–Mayagoitia; W. Scott Thornton; Jeff R. Hammond; Robert J. Harrison
      Pages: 3 - 24
      Abstract: Publication date: 2014
      Source:Annual Reports in Computational Chemistry, Volume 10
      Author(s): Álvaro Vázquez–Mayagoitia , W. Scott Thornton , Jeff R. Hammond , Robert J. Harrison
      Multiresolution analysis (MRA) is a general-purpose numerical framework to solve integral and partial differential equations that has proven to be especially successful in applications in physics and chemistry. MRA allows construction of an orthonormal basis with dynamic adaptive resolution and systematic improvability, hence, providing guaranteed finite precision. Sparse representation of many kernels allows for efficient computation. Multiresolution Adaptive Numerical Environment for Scientific Simulation code uses MRA in a multiwavelet basis with low-rank separation of functions and operators for efficient computation in many dimensions. In this chapter, we describe some of the key elements of this approach, some of its applications in chemistry (including static and time-dependent problems) and examine some of its strengths and weaknesses.

      PubDate: 2014-12-07T07:53:29Z
      DOI: 10.1016/b978-0-444-63378-1.00001-x
      Issue No: Vol. 10 (2014)
       
  • Chapter Two On the Transferability of Three Water Models Developed by
           Adaptive Force Matching
    • Authors: Hongyi Hu; Zhonghua Ma; Feng Wang
      Pages: 25 - 43
      Abstract: Publication date: 2014
      Source:Annual Reports in Computational Chemistry, Volume 10
      Author(s): Hongyi Hu , Zhonghua Ma , Feng Wang
      Water is perhaps the most simulated liquid. Recently, three water models have been developed following the adaptive force matching (AFM) method that provides excellent predictions of water properties with only electronic structure information as a reference. Compared to many other electronic structure-based force fields that rely on fairly sophisticated energy expressions, the AFM water models use point-charge-based energy expressions that are supported by most popular molecular dynamics packages. An outstanding question regarding simple force fields is whether such force fields provide reasonable transferability outside of their conditions of parameterization. A survey of three AFM water models, B3LYPD-4F, BLYPSP-4F, and WAIL, are provided for simulations under conditions ranging from the melting point up to the critical point. By including ice-Ih configurations in the training set, the WAIL potential predicts the melting temperate, T M, of ice-Ih correctly. Without training for ice, BLYPSP-4F underestimates T M by about 15K. Interestingly, the B3LYPD-4F model gives a T M 14K too high. The overestimation of T M by B3LYPD-4F mostly likely reflects a deficiency of the B3LYP reference. The BLYPSP-4F model gives the best estimate of the boiling temperature T B and is arguably the best potential for simulating water in the temperature range from T M to T B. None of the three AFM potentials provides a good description of the critical point. Although the B3LYPD-4F model gives the correct critical temperature T C and critical density ρ C, there are good reasons to believe that the agreement is reached fortuitously. Links to Gromacs input files for the three water models are provided at the end of the chapter.

      PubDate: 2014-12-07T07:53:29Z
      DOI: 10.1016/b978-0-444-63378-1.00002-1
      Issue No: Vol. 10 (2014)
       
  • Chapter Four A Microscopic View of the Mechanisms of Active Transport
           Across the Cellular Membrane
    • Authors: Giray Enkavi; Jing Li; Pochao Wen; Sundarapandian Thangapandian; Mahmoud Moradi; Tao Jiang; Wei Han; Emad Tajkhorshid
      Pages: 77 - 125
      Abstract: Publication date: 2014
      Source:Annual Reports in Computational Chemistry, Volume 10
      Author(s): Giray Enkavi , Jing Li , Pochao Wen , Sundarapandian Thangapandian , Mahmoud Moradi , Tao Jiang , Wei Han , Emad Tajkhorshid
      Membrane transporters are molecular machines that couple active transport of their specific substrates to various sources of cellular energy through a set of highly coordinated protein conformational changes. The alternating-access mechanism of transport in these proteins, which ensures that the substrate is only accessible from one side of the membrane at any given time, relies on complex and global protein conformational changes that are also closely coupled to molecular events such as substrate binding and translocation. In this review, we describe the application of advanced molecular modeling and simulation technologies to a number of membrane transport proteins studied in our laboratory. The goal is to demonstrate the power of the methods in describing functionally relevant molecular events ranging from more localized events such as substrate binding and gating motions to large, global protein conformational changes governing the transition of the protein between major functional states.

      PubDate: 2014-12-07T07:53:29Z
      DOI: 10.1016/b978-0-444-63378-1.00004-5
      Issue No: Vol. 10 (2014)
       
  • Chapter Six The Development and Implementation of a Biomolecular Docking
           Exercise for the General Chemistry Laboratory
    • Authors: Clare E. O’Grady; Peter Talpey; Timothy E. Elgren; Adam W. Van Wynsberghe
      Pages: 167 - 187
      Abstract: Publication date: 2014
      Source:Annual Reports in Computational Chemistry, Volume 10
      Author(s): Clare E. O’Grady , Peter Talpey , Timothy E. Elgren , Adam W. Van Wynsberghe
      Computational chemistry has become a widely used tool in nearly all subdisciplines of chemistry. Therefore, it is essential that students be exposed to these techniques throughout the undergraduate curriculum. In this work, we present a biomacromolecular docking laboratory exercise aimed at introducing computational physical chemistry in the context of protein-ligand binding to first-semester freshmen introductory chemistry students. The exercise focuses on investigating the binding properties of persistent organic pollutants, in particular, bisphenol A and its metabolite bisphenol-A glucuronide to estrogen receptors. This report gives a description of the exercise, its goals, and the software tools that were used to implement the laboratory activities. Importantly, all aspects of the exercise can be accomplished using freely accessible software and web servers. The success of the exercise was assessed using pre- and posttesting of conceptual and factual content and Likert scale student attitudinal surveys.

      PubDate: 2014-12-07T07:53:29Z
      DOI: 10.1016/b978-0-444-63378-1.00006-9
      Issue No: Vol. 10 (2014)
       
  • Chapter Three Seeing the Forest in Lieu of the Trees Continuum Simulations
           of Cell Membranes at Large Length Scales
    • Authors: Kayla Sapp; Roie Shlomovitz Lutz Maibaum
      Abstract: Publication date: 2014
      Source:Annual Reports in Computational Chemistry, Volume 10
      Author(s): Kayla Sapp , Roie Shlomovitz , Lutz Maibaum
      Biological membranes exhibit long-range spatial structure in both chemical composition and geometric shape, which gives rise to remarkable physical phenomena and important biological functions. Continuum models that describe these effects play an important role in our understanding of membrane biophysics at large length scales. We review the mathematical framework used to describe both composition and shape degrees of freedom, and present best practices to implement such models in a computer simulation. We discuss in detail two applications of continuum models of cell membranes: the formation of microemulsion and modulated phases and the effect of membrane-mediated interactions on the assembly of membrane proteins.

      PubDate: 2014-12-07T07:53:29Z
       
  • Chapter Five Monte Carlo Simulation of Electrolyte Solutions in Biology In
           and Out of Equilibrium
    • Authors: Boda
      Abstract: Publication date: 2014
      Source:Annual Reports in Computational Chemistry, Volume 10
      Author(s): Dezső Boda
      A concise account is given about Monte Carlo (MC) simulation techniques for homogeneous and inhomogeneous systems of electrolyte solutions at concentrations characteristic of biological situations. While the techniques are quite general, the focus here is on reduced models of ion channels where the electrolyte is modeled in the implicit solvent framework, while the channel and the membrane are modeled using minimal structural information. The ion channels under consideration are the L-type calcium channel (present in muscle cell membranes) and the ryanodine receptor calcium release channel (present in the membrane of the sarcoplasmic reticulum). Although MC simulations are known to be appropriate to simulate equilibrium systems, these examples show how to use MC techniques to simulate nonequilibrium ionic transport. The Local Equilibrium Monte Carlo method is shown to be especially useful to simulate globally nonequilibrium systems by coupling MC to the Nernst–Planck transport equation.

      PubDate: 2014-12-07T07:53:29Z
       
  • Cumulative Index
    • Abstract: Publication date: 2014
      Source:Annual Reports in Computational Chemistry, Volume 10


      PubDate: 2014-12-07T07:53:29Z
       
 
 
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