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  Subjects -> CHEMISTRY (Total: 765 journals)
    - ANALYTICAL CHEMISTRY (45 journals)
    - CHEMISTRY (530 journals)
    - CRYSTALLOGRAPHY (22 journals)
    - ELECTROCHEMISTRY (25 journals)
    - INORGANIC CHEMISTRY (40 journals)
    - ORGANIC CHEMISTRY (40 journals)
    - PHYSICAL CHEMISTRY (63 journals)

CHEMISTRY (530 journals)            First | 1 2 3 4 5 6 | Last

Glycobiology Insights     Open Access   (Followers: 1)
Graphene     Open Access   (Followers: 9)
Green and Sustainable Chemistry     Open Access   (Followers: 3)
Green Chemistry Letters and Reviews     Open Access   (Followers: 4)
Green Processing and Synthesis     Full-text available via subscription   (Followers: 1)
Handbook of Exploration and Environmental Geochemistry     Full-text available via subscription   (Followers: 1)
Handbook of Exploration Geochemistry     Full-text available via subscription  
Handbook of Surface Science     Full-text available via subscription   (Followers: 2)
Handbook of Vapor Pressure     Full-text available via subscription  
Helvetica Chimica Acta     Hybrid Journal   (Followers: 9)
Heritage Science     Open Access   (Followers: 1)
Heteroatom Chemistry     Hybrid Journal   (Followers: 2)
High Energy Chemistry     Hybrid Journal  
Indian Chemical Engineer     Hybrid Journal   (Followers: 3)
Indian Journal of Chemical Technology (IJCT)     Open Access   (Followers: 12)
Indian Journal of Chemistry - Section B (IJC-B)     Open Access   (Followers: 4)
Indian Journal of Natural Products and Resources (IJNPR)     Open Access   (Followers: 3)
Industrial & Engineering Chemistry     Full-text available via subscription   (Followers: 9)
Industrial Chemistry Library     Full-text available via subscription   (Followers: 4)
Inorganic Chemistry     Full-text available via subscription   (Followers: 18)
Inorganic Chemistry Communications     Hybrid Journal   (Followers: 7)
Inorganic Materials     Hybrid Journal   (Followers: 2)
Inorganica Chimica Acta     Hybrid Journal   (Followers: 4)
Instrumentation Science & Technology     Hybrid Journal   (Followers: 3)
International Archives of Science and Technology     Open Access  
International Journal for Ion Mobility Spectrometry     Hybrid Journal   (Followers: 1)
International Journal of Adhesion and Adhesives     Hybrid Journal   (Followers: 10)
International Journal of Bioassays     Open Access   (Followers: 5)
International Journal of Biological and Chemical Sciences     Open Access   (Followers: 2)
International Journal of Biological Chemistry     Open Access   (Followers: 4)
International Journal of Biomedical Nanoscience and Nanotechnology     Hybrid Journal   (Followers: 4)
International Journal of Carbohydrate Chemistry     Open Access   (Followers: 7)
International Journal of Chemical and Analytical Science     Full-text available via subscription   (Followers: 2)
International Journal of Chemical and Life Sciences     Open Access   (Followers: 3)
International Journal of Chemical Kinetics     Hybrid Journal   (Followers: 5)
International Journal of Chemical Technology     Open Access   (Followers: 3)
International Journal of Chemistry     Open Access   (Followers: 7)
International Journal of Chemoinformatics and Chemical Engineering     Full-text available via subscription   (Followers: 2)
International Journal of Corrosion     Open Access   (Followers: 10)
International Journal of High Throughput Screening     Open Access   (Followers: 1)
International Journal of Medicinal Chemistry     Open Access   (Followers: 7)
International Journal of Minerals, Metallurgy, and Materials     Hybrid Journal   (Followers: 6)
International Journal of Molecular Imaging     Open Access   (Followers: 1)
International Journal of Molecular Sciences     Open Access   (Followers: 1)
International Journal of Nano Dimension     Open Access  
International Journal of Nonferrous Metallurgy     Open Access  
International Journal of Photoenergy     Open Access   (Followers: 2)
International Journal of Physical Sciences     Open Access  
International Journal of Spray and Combustion Dynamics     Full-text available via subscription   (Followers: 5)
International Journal of Tryptophan Research     Open Access  
Iranian Polymer Journal     Hybrid Journal   (Followers: 4)
Israel Journal of Chemistry     Full-text available via subscription   (Followers: 2)
ISRN Environmental Chemistry     Open Access  
JBIC Journal of Biological Inorganic Chemistry     Hybrid Journal   (Followers: 2)
JCP : BioChemical Physics     Hybrid Journal  
JOT Journal für Oberflächentechnik     Hybrid Journal  
JOT-International Surface Technology     Hybrid Journal   (Followers: 1)
Journal of Chemical Engineering & Process Technology     Open Access   (Followers: 2)
Journal of Chromatography & Separation Techniques     Open Access   (Followers: 7)
Journal of Microbial & Biochemical Technology     Open Access   (Followers: 1)
Journal of Thermodynamics & Catalysis     Open Access   (Followers: 3)
Journal of Adhesion     Hybrid Journal   (Followers: 7)
Journal of Adhesion Science and Technology     Hybrid Journal   (Followers: 6)
Journal of Advanced Oxidation Technologies     Full-text available via subscription   (Followers: 1)
Journal of Advances in Chemistry     Open Access   (Followers: 2)
Journal of Agricultural and Food Chemistry     Full-text available via subscription   (Followers: 15)
Journal of Amino Acids     Open Access   (Followers: 3)
Journal of Analytical Sciences, Methods and Instrumentation     Open Access   (Followers: 1)
Journal of AOAC International     Full-text available via subscription   (Followers: 8)
Journal of Applied Chemistry     Open Access  
Journal of Applied Spectroscopy     Hybrid Journal   (Followers: 7)
Journal of Automated Methods and Management in Chemistry     Open Access  
Journal of Biomaterials and Nanobiotechnology     Open Access   (Followers: 3)
Journal of Carbohydrate Chemistry     Hybrid Journal   (Followers: 4)
Journal of Catalysis     Hybrid Journal   (Followers: 5)
Journal of Catalysts     Open Access  
Journal of Chemical & Engineering Data     Full-text available via subscription   (Followers: 6)
Journal of Chemical Education     Full-text available via subscription   (Followers: 13)
Journal of Chemical Health Risks     Open Access   (Followers: 2)
Journal of Chemical Information and Modeling     Full-text available via subscription   (Followers: 5)
Journal of Chemical Research     Full-text available via subscription   (Followers: 5)
Journal of Chemical Science and Technology     Open Access   (Followers: 1)
Journal of Chemical Sciences     Partially Free   (Followers: 13)
Journal of Chemical Theory and Computation     Full-text available via subscription   (Followers: 9)
Journal of Cheminformatics     Open Access   (Followers: 1)
Journal of Chemistry     Open Access   (Followers: 3)
Journal of Chemometrics     Hybrid Journal   (Followers: 10)
Journal of Chromatography A     Hybrid Journal   (Followers: 44)
Journal of Chromatography Library     Full-text available via subscription   (Followers: 5)
Journal of Colloid and Interface Science     Hybrid Journal   (Followers: 11)
Journal of Computational Chemistry     Hybrid Journal   (Followers: 13)
Journal of Coordination Chemistry     Hybrid Journal   (Followers: 1)
Journal of Dispersion Science and Technology     Hybrid Journal  
Journal of Encapsulation and Adsorption Sciences     Open Access   (Followers: 5)
Journal of Environmental Chemistry and Ecotoxicology     Open Access   (Followers: 2)
Journal of Flow Chemistry     Full-text available via subscription   (Followers: 1)
Journal of Fluorescence     Hybrid Journal   (Followers: 3)
Journal of Fluorine Chemistry     Hybrid Journal   (Followers: 6)
Journal of Fuel Chemistry and Technology     Full-text available via subscription   (Followers: 5)
Journal of Great Lakes Research     Hybrid Journal   (Followers: 7)

  First | 1 2 3 4 5 6 | Last

Journal Cover Journal of Theoretical and Computational Chemistry
   [9 followers]  Follow    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
     ISSN (Print) 0219-6336 - ISSN (Online) 1793-6888
     Published by World Scientific Homepage  [114 journals]   [SJR: 0.286]   [H-I: 16]
  • Recent progress in adapting Poisson–Boltzmann methods to molecular
           simulations
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 13, Issue 03, May 2014. Electrostatic solvation modeling based upon the Poisson–Boltzmann equation is widely used in studies of biomolecular structures and functions. This manuscript provides a thorough review of published efforts to adapt the numerical Poisson–Boltzmann methods to molecular simulations so that these methods can be extended to biomolecular studies involving conformational fluctuation and/or dynamics. We first review the fundamental works on how to define the electrostatic free energy and the Maxwell stress tensor. These topics are followed by three different strategies in developing algorithms to compute electrostatic forces and how to improve their numerical performance. Finally procedures are also presented in detail on how to discretize these algorithms for numerical calculations. Given the pioneer works reviewed here, further developmental efforts will be on how to balance efficiency and accuracy in these theoretical sound approaches — two important issues in applying any numerical algorithms for routine biomolecular applications. Even if not reviewed here, more advanced numerical solvers are certainly necessary to achieve higher accuracy than the widely used classical methods to improve the overall performance of the numerical Poisson–Boltzmann methods. Deformation of the disk volume element in deriving the Maxwell stress tensor. We showed that the formulations derived from the virtual deformation of the disk volume element requires a weaker condition for its validity, applicable to nonlinear Poisson–Boltzmann systems with a finite number of singularities such as atomic point charges and the existence of discontinuous dielectric as in the widely used classical piece-wise constant dielectric models.
      PubDate: Thu, 29 May 2014 07:17:00 GMT
       
  • Structural heterogeneity among four subunits in pyranose 2-oxidase: A
           molecular dynamics simulation study
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 13, Issue 03, May 2014. The homotetramer pyranose 2-oxidase (P2O) from Tetrametes multicolor contains flavin adenine dinucleotide (FAD) as a cofactor, and displays two conformers with different transient fluorescence spectra and lifetimes (ca. 0.1 ps and 360 ps). The ultrashort lifetimes of isoalloxazine (Iso) are ascribed to the photoinduced electron transfer (ET) from Trp168 to the excited Iso. Here, the structural heterogeneity among the four subunits in solution was studied by means of molecular dynamics simulation (MDS). The ET donor–acceptor distances in crystal and solution were compared. The distribution of the H-bond distances between Iso and the surrounding amino acids revealed appreciable differences among the four subunits. The structural fluctuations in two distant places were examined for the Iso-P and Iso-Q distances (where P and Q are Trp or Tyr) with the correlation coefficients between Iso-P and Iso-Q distances, revealing cooperative motions even though P and Q were more than 1 nm apart and located in different subunits. Moreover, distributions of the distances between Iso and its closest ionic amino acids markedly differed among the four subunits. Electrostatic (ES) energies between the Iso anion and the ionic amino acids in the entire protein were obtained using a static dielectric constant of 1. The ES energy in each subunit was strongly influenced by the other subunits, whilst the distributions of the ES energies greatly differed among the four subunits. This heterogeneous distribution of the ES energy between subunits may contribute to the large differences in the experimentally detected ET rates. The explicit-solvent MD simulation of homotetramer pyranose 2-oxidase shows several conformational heterogeneities. The ES energy was quite different among the four subunits and strongly influenced by the other subunits. This heterogeneous of the ES energy may contribute to the large differences in the experimentally detected electron transfer rates.
      PubDate: Thu, 29 May 2014 07:16:03 GMT
       
  • Special issue: Electrostatics and polarization effects in biophysical
           chemistry: In silico and in vitro
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print.
      PubDate: Mon, 28 Apr 2014 10:06:48 GMT
       
  • A density functional theory study of the hydration of calcium ions
           confined in the interlayer space of montmorillonites
    • Authors: sales@wspc.com.sg (Zhaoyang Lou)
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The structures of Ca2+ hydrates in the interlayer space of montmorillonites (MMT) were studied by periodic density functional theory (DFT) calculations under the GGA/PBE approximation. Affected by the internal surfaces, which are rich of negative charge, the Ca2+ hydration exhibits different behaviors from that in gas phase. The Ca2+ is located at the six-oxygen-ring (SOR) on the internal surface in dry MMT, while the incoming water molecules bind with the Ca2+, the O atoms on surface, and/or with each other. The water molecules have a tendency of forming a hydrogen bond (HB) network that connects the upper and lower surfaces. Attracted by surrounding water molecules, the Ca2+ gradually moves outward with increasing number of water molecules. Moreover, the hydration energy (EH) of Ca2+ is determined not only by the interaction between Ca2+ and H2O, but also by that among Ca2+, H2O and the surfaces. As a result, the EH has only small changes for additional incoming water molecules, in contrast to the great and monotonic decrease in gas phase.
      PubDate: Mon, 28 Apr 2014 03:58:29 GMT
       
  • Structural stabilities and transformations in cationized asparagine at
           finite temperatures: An ab initio molecular dynamics study
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print. The cationic complexes of Asparagine (Asn), M+(Asn), with M+ = Li+, Na+, K+, Cs+, and H+, are models for studying the interaction between cations and Asn. Ab initio molecular dynamics (AIMD) method is employed to simulate their behavior at finite temperatures. Structural transformation between conformers is observed, which becomes progressively easier as the cation varies from Li+, to Na+, K+, Cs+, and H+. The fluctuation of the M+–N and M+–O distances and rotation of torsional angles are significant even at room temperature for K+, Cs+ and H+. Vibrational profiles based on AIMD trajectories provide insights into the broadening and shifts in relative intensities observed in the vibrational spectra measured by infrared multi-photon dissociation (IRMPD) experiments.
      PubDate: Fri, 21 Mar 2014 09:11:46 GMT
       
  • Folding simulation of Trp-cage utilizing a new AMBER compatible force
           field with coupled main chain torsions
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print. A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER032D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity Cv is only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032D is an accurate force field that can be used for protein folding simulations.
      PubDate: Fri, 21 Mar 2014 09:11:46 GMT
       
  • Theoretical investigations of structures and properties of Au and S
           substituted poly (2,3-di-(4′-hydroxyphenyl)-1,4-phenylene ethynyl)
           at different electric field intensities
    • Authors: sales@wspc.com.sg (Jian Zhang)
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Theoretical investigations on Au and S substituted poly (2,3-di-(4′-hydroxyphenyl)-1,4-phenylene ethynyl) as a molecular wire have been carried out by incorporating the external electric field (EF). The results demonstrate that both geometric and electronic structures of conjugated molecular wire are sensitive to EF. The Z component of the dipole moment and total dipole moment increases continuously since EF polarizes the molecule. Static EF modifies the frontline molecular orbitals and HLG. The I-V curve indicates the symmetrical trend respect to the original point.
      PubDate: Fri, 21 Mar 2014 09:11:45 GMT
       
  • A density functional approach toward structural features and properties of
           C20…N2X2 (X = H, F, Cl, Br, Me) molecules
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print. In this work, the interaction of C20 with N2X2 (X = H, F, Cl, Br, Me) molecules has been explored using the B3LYP, M062x methods and 6-311G(d,p) and 6-311+G(d,p) basis sets. The interaction energies (IEs) obtained with standard method were corrected by basis set superposition error (BSSE) during the geometry optimization for all molecules at the same levels of theory. It was found C20…N2H2 interaction is stronger than the interaction of other N2X2 (X = F, Cl, Br, Me) with C20. Highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) levels are illustrated by density of states spectra (DOS). The nucleus-independent chemical shifts (NICSs) confirm that C20…N2X2 molecules exhibit aromatic characteristics. Geometries obtained from DFT calculations were used to perform NBO analysis. Also, 14N NQR parameters of the C20…N2X2 molecules are predicted.
      PubDate: Fri, 21 Mar 2014 09:11:44 GMT
       
  • Theoretical study on the formation of carbon disulfide and ammonia from
           thermal decomposition products of thiourea
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print. The formation of carbon disulfide (CS2) and ammonia (NH3) from the thermal decomposition products of thiourea has been studied with MP2, and hybrid module-based density functional theory methods (B3LYP, MPW1PW91 and PBE1PBE), each in conjunction with five different basis sets (6-31+G(2d,2p), 6-311++G(2d,2p), DGDZVP, DGDZVP2 and DGTZVP). The free energy changes and activation energies for all the five primitive reactions involved in the formation of CS2 and NH3 have been compared and discussed. The results indicate that CS2 is most likely formed in a consecutive reaction path that consists of the addition of hydrogen sulfide (H2S) to isothiocyanic acid (HNCS) to generate carbamodithioic acid and subsequent decomposition of carbamodithioic acid. By contrast, thiocyanic acid (HSCN) as the structural isomer of isothiocyanic acid is not likely the source of CS2.
      PubDate: Tue, 18 Mar 2014 08:27:01 GMT
       
  • First principles study on energetic, structural, and electronic properties
           of defective g-C3N4-zz3 nanotubes
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print. The energetic, electronic and structural properties of defective g-C3N4-zz3 nanotubes are considered based on spin-polarized density-functional theory calculations. Nine basic system types with vacancy defects are characterized by their stabilization energies and band gaps. It is found that the nitrogen atom denoted as N3 is the most favorable atom for a vacancy defect. In all cases, local bond reconstruction occurs in the presence of vacancy defects. The role of C/N bond rotations on the above properties has been also investigated. The results show that N1–C3 bond rotation is the most favorable rotational defect. In addition, the electronic properties of the semiconducting g-C3N4-zz3 nanotube with defects have been studied using band structure and density of states plots.
      PubDate: Thu, 06 Mar 2014 12:41:23 GMT
       
  • On the electrostatic properties of homodimeric proteins
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print. A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology9(2):e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily in an electrostatic funnel. It is demonstrated that the electrostatic dipole moment of the dimer is predominantly perpendicular to the axis connecting the centers of the mass of the monomers. In addition, the surface points with highest potential are located in the proximity of the interfacial plane of the homodimeric complexes. These findings indicate that frequent homodimerization provides specific electrostatic features needed for the function of proteins.
      PubDate: Fri, 14 Feb 2014 08:55:05 GMT
       
  • Biological applications of classical electrostatics methods
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print. Continuum electrostatics modeling of solvation based on the Poisson–Boltzmann (PB) equation has gained wide acceptance in biomolecular applications such as energetic analysis and structural visualization. Successful application of the PB solvent models requires careful calibration of the solvation parameters. Extensive testing and validation is also important to ensure accuracy in their applications. Limitation in the continuum modeling of solvation is also a known issue in certain biomolecular applications. Growing interest in membrane systems has further spurred developmental efforts to allow inclusion of membrane in the PB solvent models. Despite their past successes due to careful parameterization, algorithm development and parallel implementation, there is still much to be done to improve their transferability from the small molecular systems upon which they were developed and validated to complex macromolecular systems as advances in technology continue to push forward, providing ever greater computational resources to researchers to study more interesting biological systems of higher complexity.
      PubDate: Fri, 14 Feb 2014 08:55:04 GMT
       
  • Accuracy of continuum electrostatic calculations based on three common
           dielectric boundary definitions
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print.
      PubDate: Thu, 23 Jan 2014 07:23:24 GMT
       
  • Protein's native structure is dynamically stabilized by electronic
           polarization
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print.
      PubDate: Wed, 15 Jan 2014 03:25:28 GMT
       
  • Distinct mechanisms of a phosphotyrosyl peptide binding to two SH2 domains
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print.
      PubDate: Wed, 08 Jan 2014 07:52:04 GMT
       
  • Sodium versus potassium effects on the glutamic acid side-chains
           interaction on an heptapeptide
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print.
      PubDate: Wed, 08 Jan 2014 07:52:03 GMT
       
  • Modified poisson–boltzmann equations for characterizing biomolecular
           solvation
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print.
      PubDate: Mon, 23 Dec 2013 09:08:54 GMT
       
  • On the modeling of polar component of solvation energy using smooth
           Gaussian-based dielectric function
    • Abstract: Journal of Theoretical and Computational Chemistry, Volume 0, Issue 0, Ahead of Print.
      PubDate: Sat, 14 Dec 2013 08:22:34 GMT
       
 
 
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