International Journal of Molecular Sciences

1842 KiB

Open AccessReview

CFD Studies on Biomass Thermochemical Conversion

by Yiqun Wang and Lifeng Yan

Int. J. Mol. Sci. 2008, 9(6), 1108-1130; https://doi.org/10.3390/ijms9061108 - 27 Jun 2008

Cited by 100 | Viewed by 16560

Thermochemical conversion of biomass offers an efficient and economically process to provide gaseous, liquid and solid fuels and prepare chemicals derived from biomass. Computational fluid dynamic (CFD) modeling applications on biomass thermochemical processes help to optimize the design and operation of thermochemical reactors. [...] Read more.

Thermochemical conversion of biomass offers an efficient and economically process to provide gaseous, liquid and solid fuels and prepare chemicals derived from biomass. Computational fluid dynamic (CFD) modeling applications on biomass thermochemical processes help to optimize the design and operation of thermochemical reactors. Recent progression in numerical techniques and computing efficacy has advanced CFD as a widely used approach to provide efficient design solutions in industry. This paper introduces the fundamentals involved in developing a CFD solution. Mathematical equations governing the fluid flow, heat and mass transfer and chemical reactions in thermochemical systems are described and sub-models for individual processes are presented. It provides a review of various applications of CFD in the biomass thermochemical process field. Full article

(This article belongs to the Special Issue Biofuels R&D: Securing the Planet's Future Energy Needs)

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297 KiB

Open AccessReview

Betulinic Acid for Cancer Treatment and Prevention

by Simone Fulda

Int. J. Mol. Sci. 2008, 9(6), 1096-1107; https://doi.org/10.3390/ijms9061096 - 27 Jun 2008

Cited by 308 | Viewed by 20340

Abstract

Betulinic acid is a natural product with a range of biological effects, for example potent antitumor activity. This anticancer property is linked to its ability to induce apoptotic cell death in cancer cells by triggering the mitochondrial pathway of apoptosis. In contrast to [...] Read more.

Betulinic acid is a natural product with a range of biological effects, for example potent antitumor activity. This anticancer property is linked to its ability to induce apoptotic cell death in cancer cells by triggering the mitochondrial pathway of apoptosis. In contrast to the cytotoxicity of betulinic acid against a variety of cancer types, normal cells and tissue are relatively resistant to betulinic acid, pointing to a therapeutic window. Compounds that exert a direct action on mitochondria present promising experimental cancer therapeutics, since they may trigger cell death under circumstances in which standard chemotherapeutics fail. Thus, mitochondrion-targeted agents such as betulinic acid hold great promise as a novel therapeutic strategy in the treatment of human cancers. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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728 KiB

Open AccessReview

Density Functionals of Chemical Bonding

by Mihai V. Putz

Int. J. Mol. Sci. 2008, 9(6), 1050-1095; https://doi.org/10.3390/ijms9061050 - 26 Jun 2008

Cited by 48 | Viewed by 15571

Abstract

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps [...] Read more.

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. Full article

(This article belongs to the Special Issue The Chemical Bond and Bonding)

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864 KiB

Open AccessReview

Targeting Receptor Tyrosine Kinases for Chemoprevention by Green Tea Catechin, EGCG

by Masahito Shimizu, Yohei Shirakami and Hisataka Moriwaki

Int. J. Mol. Sci. 2008, 9(6), 1034-1049; https://doi.org/10.3390/ijms9061034 - 20 Jun 2008

Cited by 92 | Viewed by 15741

Abstract

Tea is one of the most popular beverages consumed worldwide. Epidemiologic studies show an inverse relationship between consumption of tea, especially green tea, and development of cancers. Numerous in vivo and in vitro studies indicate strong chemopreventive effects for green tea and its [...] Read more.

Tea is one of the most popular beverages consumed worldwide. Epidemiologic studies show an inverse relationship between consumption of tea, especially green tea, and development of cancers. Numerous in vivo and in vitro studies indicate strong chemopreventive effects for green tea and its constituents against cancers of various organs. (–)-Epigallocatechin-3-gallate (EGCG), the major catechin in green tea, appears to be the most biologically active constituent in tea with respect to inhibiting cell proliferation and inducing apoptosis in cancer cells. Recent studies indicate that the receptor tyrosine kinases (RTKs) are one of the critical targets of EGCG to inhibit cancer cell growth. EGCG inhibits the activation of EGFR (erbB1), HER2 (neu/erbB2) and also HER3 (neu/erbB3), which belong to subclass I of the RTK superfamily, in various types of human cancer cells. The activation of IGF-1 and VEGF receptors, the other members of RTK family, is also inhibited by EGCG. In addition, EGCG alters membrane lipid organization and thus inhibits the dimerization and activation of EGFR. Therefore, EGCG inhibits the Ras/MAPK and PI3K/Akt signaling pathways, which are RTK-related cell signaling pathways, as well as the activation of AP-1 and NF-κB, thereby modulating the expression of target genes which are associated with induction of apoptosis and cell cycle arrest in cancer cells. These findings are significant because abnormalities in the expression and function of RTKs and their downstream effectors play a critical role in the development of several types of human malignancies. In this paper we review evidence indicating that EGCG exerts anticancer effects, at least in part, through inhibition of activation of the specific RTKs and conclude that targeting RTKs and related signaling pathway by tea catechins might be a promising strategy for the prevention of human cancers. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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2421 KiB

Open AccessArticle

Ion-Molecule Reactions and Chemical Composition of Emanated from Herculane Spa Geothermal Sources

by Constantin Cosma, Ioan Suciu, Lorentz Jäntschi and Sorana D. Bolboacă

Int. J. Mol. Sci. 2008, 9(6), 1024-1033; https://doi.org/10.3390/ijms9061024 - 20 Jun 2008

Cited by 6 | Viewed by 8932

Abstract

The paper presents a chemical composition analysis of the gases emanated from geothermal sources in the Herculane Spa area (Romania). The upper homologues of methane have been identified in these gases. An ion-molecule reaction mechanism could be implicated in the formation of the [...] Read more.

The paper presents a chemical composition analysis of the gases emanated from geothermal sources in the Herculane Spa area (Romania). The upper homologues of methane have been identified in these gases. An ion-molecule reaction mechanism could be implicated in the formation of the upper homologues of methane. The CH₄⁺ ions that appear under the action of radiation are the starting point of these reactions. The presence of hydrogen in the emanated gases may be also a result of these reactions. Full article

(This article belongs to the Special Issue Green Antifouling)

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294 KiB

Open AccessArticle

Effective DNA Inhibitors of Cathepsin G by In Vitro Selection

by Barbara Gatto, Elena Vianini, Lorena Lucatello, Claudia Sissi, Danilo Moltrasio, Rodolfo Pescador, Roberto Porta and Manlio Palumbo

Int. J. Mol. Sci. 2008, 9(6), 1008-1023; https://doi.org/10.3390/ijms9061008 - 20 Jun 2008

Cited by 4 | Viewed by 10265

Abstract

Cathepsin G (CatG) is a chymotrypsin-like protease released upon degranulation of neutrophils. In several inflammatory and ischaemic diseases the impaired balance between CatG and its physiological inhibitors leads to tissue destruction and platelet aggregation. Inhibitors of CatG are suitable for the treatment of [...] Read more.

Cathepsin G (CatG) is a chymotrypsin-like protease released upon degranulation of neutrophils. In several inflammatory and ischaemic diseases the impaired balance between CatG and its physiological inhibitors leads to tissue destruction and platelet aggregation. Inhibitors of CatG are suitable for the treatment of inflammatory diseases and procoagulant conditions. DNA released upon the death of neutrophils at injury sites binds CatG. Moreover, short DNA fragments are more inhibitory than genomic DNA. Defibrotide, a single stranded polydeoxyribonucleotide with antithrombotic effect is also a potent CatG inhibitor. Given the above experimental evidences we employed a selection protocol to assess whether DNA inhibition of CatG may be ascribed to specific sequences present in defibrotide DNA. A Selex protocol was applied to identify the single-stranded DNA sequences exhibiting the highest affinity for CatG, the diversity of a combinatorial pool of oligodeoxyribonucleotides being a good representation of the complexity found in defibrotide. Biophysical and biochemical studies confirmed that the selected sequences bind tightly to the target enzyme and also efficiently inhibit its catalytic activity. Sequence analysis carried out to unveil a motif responsible for CatG recognition showed a recurrence of alternating TG repeats in the selected CatG binders, adopting an extended conformation that grants maximal interaction with the highly charged protein surface. This unprecedented finding is validated by our results showing high affinity and inhibition of CatG by specific DNA sequences of variable length designed to maximally reduce pairing/folding interactions. Full article

(This article belongs to the Special Issue Nucleic Acid Derivatives in Emerging Technologies)

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237 KiB

Open AccessArticle

Synthesis and Characterization of Some New Tetraaldehyde and Tetraketone Derivatives and X-ray Structure of 1,1'-(4,4'-(2- (1,3-bis(4-Acetylphenoxy)propan-2-ylidene)propane-1,3-diyl) bis(oxy)bis(4,1-phenylene))diethanone

by Mustafa Er, Reşat Ustabaş, Ufuk Çoruh, Kemal Sancak and Ezequiel Vázquez-López

Int. J. Mol. Sci. 2008, 9(6), 1000-1007; https://doi.org/10.3390/ijms9061000 - 13 Jun 2008

Cited by 24 | Viewed by 13528

Abstract

Tetraketone and tetraaldehyde derivatives 2a-d were synthesized via the reaction of ethene-1,1,2,2,-tetra-yl-tetramethylene tetrabromide (1) with hydroxyketone and aldehyde derivatives. The molecular structures were identifed by IR, ¹H-NMR, ¹³CNMR and MS analysis. The crystal structure of the title compound 2a, C₃₈ [...] Read more.

Tetraketone and tetraaldehyde derivatives 2a-d were synthesized via the reaction of ethene-1,1,2,2,-tetra-yl-tetramethylene tetrabromide (1) with hydroxyketone and aldehyde derivatives. The molecular structures were identifed by IR, ¹H-NMR, ¹³CNMR and MS analysis. The crystal structure of the title compound 2a, C₃₈H₃₆O₈, is reported. Its crystal data are: monoclinic, space group P 2(1)/n with cell dimensions of a= 9.0395(12) Å ,b= 12.6114(17) Å, c = 13.8166(18) Å, β= 95.875(3), V= 1566.8(4) Å³, F.W.= 620.67, ρ_calc =1.316 gcm³ for Z=2, μ=0.092 mm^-1 Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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565 KiB

Open AccessReview

MicroRNA: an Emerging Therapeutic Target and Intervention Tool

by Zhen Liu, Alhousseynou Sall and Decheng Yang

Int. J. Mol. Sci. 2008, 9(6), 978-999; https://doi.org/10.3390/ijms9060978 - 13 Jun 2008

Cited by 143 | Viewed by 16120

Abstract

MicroRNAs (miRNAs) are a class of short non-coding RNAs with posttranscriptional regulatory functions. To date, more than 600 human miRNAs have been experimentally identified, and estimated to regulate more than one third of cellular messenger RNAs. Accumulating evidence has linked the dysregulated expression [...] Read more.

MicroRNAs (miRNAs) are a class of short non-coding RNAs with posttranscriptional regulatory functions. To date, more than 600 human miRNAs have been experimentally identified, and estimated to regulate more than one third of cellular messenger RNAs. Accumulating evidence has linked the dysregulated expression patterns of miRNAs to a variety of diseases, such as cancer, neurodegenerative diseases, cardiovascular diseases and viral infections. MiRNAs provide its particular layer of network for gene regulation, thus possessing the great potential both as a novel class of therapeutic targets and as a powerful intervention tool. In this regard, synthetic RNAs that contain the binding sites of miRNA have been shown to work as a “decoy” or “miRNA sponge” to inhibit the function of specific miRNAs. On the other hand, miRNA expression vectors have been used to restore or overexpress specific miRNAs to achieve a long-term effect. Further, double-stranded miRNA mimetics for transient replacement have been experimentally validated. Endogenous precursor miRNAs have also been used as scaffolds for the induction of RNA interference. This article reviews the recent progress on this emerging technology as a powerful tool for gene regulation studies and particularly as a rationale strategy for design of therapeutics. Full article

(This article belongs to the Special Issue Nucleic Acid Derivatives in Emerging Technologies)

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267 KiB

Open AccessArticle

A New Approach on Estimation of Solubility and n-Octanol/ Water Partition Coefficient for Organohalogen Compounds

by Shuo Gao and Chenzhong Cao

Int. J. Mol. Sci. 2008, 9(6), 962-977; https://doi.org/10.3390/ijms9060962 - 2 Jun 2008

Cited by 11 | Viewed by 9532

Abstract

The aqueous solubility (logW) and n-octanol/water partition coefficient (logP_OW) are important properties for pharmacology, toxicology and medicinal chemistry. Based on an understanding of the dissolution process, the frontier orbital interaction model was suggested in the present paper to describe the solvent-solute [...] Read more.

The aqueous solubility (logW) and n-octanol/water partition coefficient (logP_OW) are important properties for pharmacology, toxicology and medicinal chemistry. Based on an understanding of the dissolution process, the frontier orbital interaction model was suggested in the present paper to describe the solvent-solute interactions of organohalogen compounds and a general three-parameter model was proposed to predict the aqueous solubility and n-octanol/water partition coefficient for the organohalogen compounds containing nonhydrogen-binding interactions. The model has satisfactory prediction accuracy. Furthermore, every item in the model has a very explicit meaning, which should be helpful to understand the structure-solubility relationship and may be provide a new view on estimation of solubility. Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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329 KiB

Open AccessArticle

Prodrugs of Fluoro-Substituted Benzoates of EGC as Tumor Cellular Proteasome Inhibitors and Apoptosis Inducers

by Zhiyong Yu, Xu Long Qin, Yan Yan Gu, Di Chen, Qiuzhi Cindy Cui, Tao Jiang, Sheng Biao Wan and Q. Ping Dou

Int. J. Mol. Sci. 2008, 9(6), 951-961; https://doi.org/10.3390/ijms9060951 - 2 Jun 2008

Cited by 17 | Viewed by 12650

Abstract

The most potent catechin in green tea is (-)-epigallocatechin-3-gallate [(-)- EGCG], which, however, is unstable under physiological conditions. To discover more stable and more potent polyphenol proteasome inhibitors, we synthesized several novel fluoro-substituted (-)-EGCG analogs, named F-EGCG analogs, as well as their prodrug [...] Read more.

The most potent catechin in green tea is (-)-epigallocatechin-3-gallate [(-)- EGCG], which, however, is unstable under physiological conditions. To discover more stable and more potent polyphenol proteasome inhibitors, we synthesized several novel fluoro-substituted (-)-EGCG analogs, named F-EGCG analogs, as well as their prodrug forms with all of -OH groups protected by acetate. We report that the prodrug form of one F-EGCG analog exhibited greater potency than the previously reported peracetate of (-)- EGCG to inhibit proteasomal activity, suppress cell proliferation, and induce apoptosis in human leukemia Jurkat T cells, demonstrating the potential of these compounds to be developed into novel anti-cancer and cancer-preventive agents. Full article

(This article belongs to the Special Issue Structure-Property/Activity Modeling of Polyphenols)

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367 KiB

Open AccessArticle

Cloning, Expression, Purification and Crystallization of the PR Domain of Human Retinoblastoma Protein-Binding Zinc Finger Protein 1 (RIZ1)

by Wanpeng Sun, C. Ronald Geyer and Jian Yang

Int. J. Mol. Sci. 2008, 9(6), 943-950; https://doi.org/10.3390/ijms9060943 - 2 Jun 2008

Cited by 8 | Viewed by 9953

Abstract

Through alternative promoter usage, human retinoblastoma protein-interacting zinc finger gene RIZ encodes two different protein products, RIZ1 and RIZ2, which have been identified to be a tumor suppressor and a proto-oncoprotein, respectively. Structurally, the two protein products share the same amino acid sequences [...] Read more.

Through alternative promoter usage, human retinoblastoma protein-interacting zinc finger gene RIZ encodes two different protein products, RIZ1 and RIZ2, which have been identified to be a tumor suppressor and a proto-oncoprotein, respectively. Structurally, the two protein products share the same amino acid sequences except that RIZ2 lacks an N-terminal PR domain with methyltransferase activity. Previous studies have shown that over-expression of RIZ2 is usually associated with depressed RIZ1 expression in different human cancers. It is generally believed that RIZ1 and RIZ2 regulate normal cell division and function using a “Yin-Yang” fashion and the PR domain is responsible for the tumor suppressing activity of RIZ1. In order to better understand the biological functions of the PR domain by determining its three-dimensional crystal structure, we expressed, purified and crystallized a construct of the PR domain (amino acid residues 13-190) in this study. The maximum size of the needle-shaped crystals was approximately 0.20 x 0.01 x 0.01 mm. Full article

(This article belongs to the Special Issue Protein Crystallography)

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481 KiB

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Bonding in Mercury-Alkali Molecules: Orbital-driven van der Waals Complexes

by Elfi Kraka and Dieter Cremer

Int. J. Mol. Sci. 2008, 9(6), 926-942; https://doi.org/10.3390/ijms9060926 - 2 Jun 2008

Cited by 7 | Viewed by 10716

Abstract

The bonding situation in mercury-alkali diatomics HgA (²Σ⁺) (A = Li, Na, K, Rb) has been investigated employing the relativistic all-electron method Normalized Elimination of the Small Component (NESC), CCSD(T), and augmented VTZ basis sets. Although Hg,A interactions are [...] Read more.

The bonding situation in mercury-alkali diatomics HgA (²Σ⁺) (A = Li, Na, K, Rb) has been investigated employing the relativistic all-electron method Normalized Elimination of the Small Component (NESC), CCSD(T), and augmented VTZ basis sets. Although Hg,A interactions are typical of van der Waals complexes, trends in calculated De values can be explained on the basis of a 3-electron 2-orbital model utilizing calculated ionization potentials and the De values of HgA⁺(¹Σ⁺) diatomics. HgA molecules are identified as orbital-driven van der Waals complexes. The relevance of results for the understanding of the properties of liquid alkali metal amalgams is discussed. Full article

(This article belongs to the Special Issue The Chemical Bond and Bonding)

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Int. J. Mol. Sci., Volume 9, Issue 6 (June 2008) – 12 articles , Pages 926-1130

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