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Search Results: 1 - 10 of 402308 matches for " Henk M. Buck "
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An Adjusted Model for Simple 1,2-Dyotropic Reactions. Ab Initio MO and VB Considerations  [PDF]
Henk M. Buck
Open Journal of Physical Chemistry (OJPC) , 2013, DOI: 10.4236/ojpc.2013.33015
Abstract:

With an adjusted model, we reconsider simple 1,2-dyotropic reactions with the introduction of a concept based on the intramolecular dynamics of a tetrahedron (van ’t Hoff modeling). In fact the dyotropic reactions are strongly related to conversions originated from neighbouring group participation or anchimeric assistance, defined as the interaction of a center with a lone pair of electrons in an atom and the electrons present in aδor π bond. The researchful 1,2-dyotropic reactions, based on the 1,2-interchange of halogens, methyl and hydrogen taking place in a concerted fashion, are in competition with the two-step reaction in which the neighbouring group participation or anchimeric assistance comes to full expression by ionic dissociation of the other exchangeable (halogen) atom. As to be expected there is an essential difference between halogen or methyl exchange regarding the number of electrons participating in the transition state. This aspect becomes evident in the geometries of the corresponding transition state geometries. In this paper we refer to ab initio MO calculations and VB considerations. We consider the 1,2-halogen exchange as a combination of two SN2 reactions each containing four electrons. The van ’t Hoff dynamics appears a useful model in order to illustrate the computations in a straightforward manner.

A conformational B-Z DNA study monitored with phosphatemethylated DNA as a model for epigenetic dynamics focused on 5-(hydroxy)methylcytosine  [PDF]
Henk M. Buck
Journal of Biophysical Chemistry (JBPC) , 2013, DOI: 10.4236/jbpc.2013.42005
Abstract:

This study was directed on the B- into Z-DNA isomerization with alternating CG sequences monitored with artificial DNA model-systems based on methylation of the phosphate backbone. The chemical concept for this transition wherein shielding of the oxygen anions of the backbone phosphates plays an essential role, resulted in the preparation of the phosphatemethylated d(CpG). Even on this primitive level of only two base pair long, the B-Z conformational aspects of this self-complementary duplex could be described in solution with nuclear magnetic resonance (NMR) and circular dichroism (CD) measurements. The exclusivity of this choice became clear after synthesizing phosphatemethylated DNA with longer alternating CG fragments. It could be shown that conflicting conformational effects of the CG and GC fragments resulted in an overall B structure of the phosphatemethylated tetramer d(CPGPCPG). From our model considerations, it is clear that the internal stress introduced by the alternating CG sequences will be promoted by a complete shielding of the phosphate backbone. Elimination of this effect may be realized by a site-specific phosphate shielding. The role of the anti-syn isomerization of G in the CG fragments is clarified by methylation of the phosphate group. This anti-syn transition is absent in corresponding methylphosphonates, suggesting an exclusive role for base-backbone coordination via hydrogen bonding. In addition, we propose that the B- into Z-DNA interconversion may offer a mechanistic view for differences in dynamics between cytosine and its epigenetic derivative 5-methylcytosine. This mechanism has been extended to the demethylation of 5-methylcytosine and the exchange of information between the new epigenetic base, 5-hydroxymethylcytosine and the DNA backbone via an intramolecular phosphorylation. The role of 5-hydroxymethylcytosine in Alzheimer disease has been briefly discussed. In our opinion, this study can be considered as a new dynamic concept for epigenetics based on the dynamics of the B-Z transition in natural and phosphatemethylated DNA.

Three-Center Configuration with Four,Three, and Two Electrons for Carbon,Boron, Hydrogen, and Halogen Exchange. A Model and Theoretical Study with Experimental Evidence  [PDF]
Henk M. Buck
Open Journal of Physical Chemistry (OJPC) , 2014, DOI: 10.4236/ojpc.2014.42006
Abstract:

The introduction of specific sites in organic frames for accommodation of various modes of bonding has been focused on reaction types which are described by using different theoretical models with or without a definite experimental proof. In this study three-center four-, three-, and two-electron systems based on carbon-, boron-, hydrogen-, and halogen exchange are under consideration. Based on the number of electrons in the transition state or transition complex it is shown that all transfer or exchange reactions share the same ratio numbers expressed as the quotient of the transitional bond distance under investigation and its normal bond length. With X-ray data of model systems it was even possible to give the ratio numbers for a three-center four-electron configuration experimental support with additional ab initio data. Furthermore a novel model type of substitution in organic chemistry is introduced through electrophilic insertion, informative for enzyme-substrate interactions based on the lock-and-key model. Reactions based on a three-center two-electron configuration mostly follow a nonlinear transition. In this alignment there will be a pursuit of cyclization for stabilization via homoaromaticity as homocyclopropenyl cation. The molecular dynamics of such a process is discussed based on recent X-ray crystallographic data of the symmetrically bridged, nonclassical geometry of the 2-norbornyl cation. In the present paper the focus is aimed at the transition intermediate of the (classical) 2-norbornyl cation involved in the isomerization into the nonclassical geometry. This model description is compared with a simple molecular rearrangement of the 1-propyl cation into the corner-protonated cyclopropane using the ab initio data. The exclusivity of the former isomerization compared with the latter one could be unambiguously demonstrated by the invention that theintramolecularelectron shift can be expressed in a linear relationship between the concerned electron-donating and accepting bond lengths. Finally, the fluor transitions as divalent atoms in a three-center two-electron configuration are described. The role of fluor in comparison with the other halogens is striking. The attention was focused on an excellent correspondence between the recent chemical and theoretical evidence for a symmetrical fluoronium ionin solution. Simple dialkylfluoroniumions in contrast to the other halonium ions are not present in solution. Although the geometry of the fluoronium ion theoretically can be described as a real minimum,

Interconversion between Planar-Triangle, Trigonal-Pyramid and Tetrahedral Configurations of Boron (B(OH)3 -B(OH)4- ), Carbon (CH3+ -CH3X) and for the Group 15 Elements as Nitrogen (NH3-NH4+ ). A Modelling Description with Ab Initio Results and Pressure-Induced Experimental Evidence  [PDF]
Henk M. Buck
Open Journal of Physical Chemistry (OJPC) , 2015, DOI: 10.4236/ojpc.2015.51001
Abstract: Recently a mechanistic understanding of the pressure-and/or temperature-induced coordination change of boron in a borosilicate glass has been demonstrated by Edwards et al. In situ high-pressure 11B solid-state NMR spectroscopy has been used in combination with ab initio calculations in order to obtain insight in the molecular geometry for the pressure-induced conversion. The results indicate a deformation of the B(OH)3 planar triangle, under isotropic stress, into a trigonal pyramid that serves as a precursor for the formation of a tetrahedral boron configuration. From our point of view, the deformation controlling the out-of-plane transition of boron accompanied with a D3h into C3v geometric change is an interesting transformation because it matches with our molecular description based on Van’t Hoff modelling for the tetrahedral change of carbon in CH3X by substitution of X with nucleophiles via a trigonal bipyramid state in which the transferred carbon is present as a methyl planar triangle “cation”. Van’t Hoff modelling and ab initio calculations have been also applied on the dynamics of the out-of-plane geometry of a transient positively charged carbon in a trigonal pyramidal configuration into a planar trivalent carbon cation. Finally the same model is also used for the C3v trigonal pyramidal configurations as NH3 of the group 15 elements in their nucleophilic abilities.
Retracted HIV Study Provides New Information about the Status of the in Vitro Inhibition of DNA Replication by Backbone Methylation  [PDF]
Henk M. Buck
Journal of Biophysical Chemistry (JBPC) , 2015, DOI: 10.4236/jbpc.2015.61003
Abstract: In this publication attention is given to a retracted article in Science at the end of 1990 concerning the HIV-1 inhibition by a modified backbone DNA as the phosphatemethylated DNA. A disproportion in the presented data resulted in a faulty generalization of the (bio)chemical characteristics of the phosphatemethylated DNA (18- and 20-nucleotides). In the confusion and the outside pressure a related study in Nucleic Acids Research on the in vitro dynamics of a regiospecific inhibition of DNA duplication with long (20- and 18-nucleotides) and short (8-nucleotides) phosphatemethylated DNA was completely ignored. A restoration will be given based on a comprehensive view demonstrating the unique molecular and conformational properties of phosphatemethylated DNA in their (bio)chemistry towards natural DNA and RNA (HIV-1 RNA loops).
Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers  [PDF]
Henk M. Buck
Journal of Biophysical Chemistry (JBPC) , 2016, DOI: 10.4236/jbpc.2016.71003
Abstract: After the recent publication in the Journal of Biophysical Chemistry entitled “Retracted HIV Study Provides New Information about the Status of the in Vitro Inhibition of DNA Replication by Back-bone Methylation”, it is of importance to review the results of Buck’s group on the synthesis and conformation analyses of phosphate-methylated RNAs in order to afford information on the absence of a further investigation with regard to this de facto acceptable approach. In fact these compounds belong to the very first group of RNAs with a modified neutral backbone by phosphatemethylation. In contrast to the corresponding phosphate-methylated DNAs with a frozen B-conformation, the phosphate-methylated RNAs show an A-conformation. The latter is a prerequisite for duplex formation with (complementary) (natural) RNA. A number of experiments support this fundamental statement. After the HIV study was retracted, the overall results concerning the phosphate-methylated RNAs were published without mentioning Buck’s initial proof of concept and his contributions. Generally, the (modified) dimer RNAs and DNAs possess a number of specific biophysical properties. A novel explanation is given for conflicting structural determinations.
A Molecular Description of Superconductivity of Sulfur Hydride and Related Systems under High-Pressure Conditions  [PDF]
Henk M. Buck
Open Journal of Physical Chemistry (OJPC) , 2017, DOI: 10.4236/ojpc.2017.71002
Abstract: It has been shown that the recently discovered sulfur trihydride (H3S) can be considered as a superconductor with a transition temperature Tc of 203 Kelvin (K) at 155 GigaPascals (GPa). This is the highest Tc value reported for any superconductor. The established superconductivity occurs via the formation of a molecular system with sulfur atoms arranged on a body-centered cubic lattice. It has been generally accepted that the high Tc value is the result of an efficient electron-phonon interaction. The responsible substance formed by H2S under high pressure, may be considered as a compound with H3S stoichiometry creating an impressive network with hydrogens. We will focus on the hydrogen bonding between sulfur and hydrogens demonstrating a symmetrical arrangement. The geometry of the individual radical compound in relation to corresponding systems will be discussed. Ab initio calculations based on a linear three-center two-, three- and four-electron type of bonding clearly visualized in combination with the dynamics of the Van’t Hoff concept, as described by us in various papers, give a good description of this exclusive network. We also discuss the superconductivity of related phosphorus hydrides and focus on the stability and geometrical differences with respect to the H3S system. These differences are significant, demonstrating the diversity in various structures in showing superconductivity.
DNA-Like Duplex Structures Derived from Chemistry Based on 2’-Deoxy-Cytidine: A New Model for Base-Specific Inhibition of G and C on DNA and RNA Level  [PDF]
Henk M. Buck
Journal of Biophysical Chemistry (JBPC) , 2018, DOI: 10.4236/jbpc.2018.93003
Abstract: The new epigenetic elements 5-hydroxymethyl-dC, 5-formyl-dC, and 5-car- boxy-dC may be considered as intermediates of an active demethylation process. A comprehensive mechanistic model is given for the C-C bond cleavage focused on the chemistry within the DNA duplex structure. In addition we register spin-off chemistry of this process in evaluating new duplex systems closely related to natural DNA and RNA concerning their hydrogen-bond symmetrization. A model is composed for a base-specific inhibition of G and C on the DNA and RNA level. C-G combinations are of general importance in controlling the dynamics of gene expression. In some way the suggested model systems are related to antisense oligonucleotides (ASOs).
One-Electron-Addition to Pentavalent Phosphorus with the Phosphorus-Chlorine Bond as Acceptor Introducing a Fundamental Distinction in Substitution Mechanism between SN2(P) and SN2(C)  [PDF]
Henk M. Buck
Open Journal of Physical Chemistry (OJPC) , 2019, DOI: 10.4236/ojpc.2019.93010
Abstract: An electron-addition, under single-crystal conditions, to pentavalent phosphorus compounds as Cl-P (=O, S) Y, Z with the P-Cl bond as electron-accepting group, is selected as an additional model for SN2(P) like reactions. It is demonstrated that the geometric information stored in the tetrahedral configuration (substrate) can be transmitted in the corresponding trigonal bipyramidal (TBP) state for nucleophilic substitution. In this article, we focus on these specific mechanistic aspects of carbon and phosphorus. We consider our study as a contribution to the significance of these (bio)chemical intermediates.
Estimating a Falsified Model  [PDF]
Andrew J. Buck, George M. Lady
Advances in Pure Mathematics (APM) , 2016, DOI: 10.4236/apm.2016.68040
Abstract: It is common econometric practice to propose a system of equations, termed the “structure,” estimate each endogenous variable in the structure via a linear regression with all of the exogenous variables as arguments, and then employ one of variety of regression techniques to recapture the coefficients in the (Jacobian) arrays of the structure. A recent literature, e.g., [1], has shown that a qualitative analysis of a model’s structural and estimated reduced form arrays can provide a robust procedure for assessing if a model’s hypothesized structure has been falsified. This paper shows that the even weaker statement of the model’s structure provided by zero restrictions on the structural arrays can be falsified, independent of the proposed nonzero entries. When this takes place, multi-stage least squares, or any procedure for estimating the structural arrays with the zero restrictions imposed, will present estimates that could not possibly have generated the data upon which the estimated reduced form is based. The examples given in the paper are based upon a Monte Carlo sampling procedure.
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