Khatcharin Siriwong - Academia.edu (original) (raw)
Papers by Khatcharin Siriwong
Journal of Thermal Analysis and Calorimetry, 2015
ABSTRACT The olivine LiNiPO4 was synthesized via the calcination of the new precursor LiNiPO4·3H2... more ABSTRACT The olivine LiNiPO4 was synthesized via the calcination of the new precursor LiNiPO4·3H2O at 600 °C. The precursor was obtained from low-temperature (50 °C) wet chemical reaction. The results from XRD, FTIR, AAS/AES and TG/DTG/DTA techniques confirmed the formula of the title compounds. The SEM results indicated the morphologies of the hydrate precursor as thin plate particles and the calcined product as small bead particles. The BET surface area of the final calcined product at 600 °C is much higher (5.807 m2 g−1) than that reported in the literature (0.25 m2 g−1). The kinetic triplet [activation energy, E, pre-exponential factor, A, and the most probable mechanism function, g(α)] and the thermodynamic functions of activated complexes (ΔS ≠, ΔH ≠ and ΔG ≠) for the dehydration step of LiNiPO4·3H2O were determined and discussed. The mechanism of the dehydration process is the single-step A3/2 (assumed random nucleation and its subsequent growth). New information, namely the isobaric molar heat capacity, experimental entropy, enthalpy and Gibbs energy changes as function of temperature (K) of LiNiPO4·3H2O and LiNiPO4, was evaluated from the DSC data by third-order polynomial fitting and reported for the first time. The calculated corresponding thermodynamic functions from kinetic parameters are compared and discussed.
Inorganica Chimica Acta, 2011
Journal of Thermal Analysis and Calorimetry, 2015
ABSTRACT The olivine LiNiPO4 was synthesized via the calcination of the new precursor LiNiPO4·3H2... more ABSTRACT The olivine LiNiPO4 was synthesized via the calcination of the new precursor LiNiPO4·3H2O at 600 °C. The precursor was obtained from low-temperature (50 °C) wet chemical reaction. The results from XRD, FTIR, AAS/AES and TG/DTG/DTA techniques confirmed the formula of the title compounds. The SEM results indicated the morphologies of the hydrate precursor as thin plate particles and the calcined product as small bead particles. The BET surface area of the final calcined product at 600 °C is much higher (5.807 m2 g−1) than that reported in the literature (0.25 m2 g−1). The kinetic triplet [activation energy, E, pre-exponential factor, A, and the most probable mechanism function, g(α)] and the thermodynamic functions of activated complexes (ΔS ≠, ΔH ≠ and ΔG ≠) for the dehydration step of LiNiPO4·3H2O were determined and discussed. The mechanism of the dehydration process is the single-step A3/2 (assumed random nucleation and its subsequent growth). New information, namely the isobaric molar heat capacity, experimental entropy, enthalpy and Gibbs energy changes as function of temperature (K) of LiNiPO4·3H2O and LiNiPO4, was evaluated from the DSC data by third-order polynomial fitting and reported for the first time. The calculated corresponding thermodynamic functions from kinetic parameters are compared and discussed.
The Journal of Physical Chemistry Letters, 2015
Molecular structures that direct charge transport in two or three dimensions possess some of the ... more Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among "well stacked" conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups ("extenders") lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA.
The Journal of Physical Chemistry C, 2010
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2012
ABSTRACT During the last two decades, electron transfer (ET) through DNA and its artificial analo... more ABSTRACT During the last two decades, electron transfer (ET) through DNA and its artificial analogues has been an area of extensive experimental and theoretical studies. This process plays an important role in biology (damage and repair of DNA in living cells) and is of potential interest in material sciences. Because structural dynamics of the π stack and its environment affect essentially the electron transport, some significant details of excess charge migration cannot be derived from experiments. Computer simulations of the ET process provide microscopic insights into mechanisms of this process. In the paper, we consider computational methods used to describe the propagation of excess charges through π stacks of DNA and related systems. © 2012 John Wiley & Sons, Ltd.
RSC Advances, 2014
ABSTRACT Nucleic acids or nucleic acid analogues carrying an environment sensitive fluorophore th... more ABSTRACT Nucleic acids or nucleic acid analogues carrying an environment sensitive fluorophore that can change optical properties in response to hybridization with complementary DNA or RNA targets are potentially useful as self-reporting hybridization probes that do not require a quencher. In this study, pyrrolidinyl peptide nucleic acids (acpcPNA) carrying a pyrene label at terminal, or internal positions were synthesized and their fluorescence properties investigated. Significant fluorescence increases, between 2.9 and 73 fold, were observed only with internally pyrene-labeled acpcPNA upon hybridization with complementary DNA under a variety of sequence contexts. Hybridization with mismatched DNA targets yielded mostly unchanged or decreased fluorescence, depending on the type and position of the mismatch base. Non-specific fluorescence increase due to the presence of a mismatch located away from the pyrene label could be eliminated by digestion with S1 nuclease, which allows unambiguous discrimination between complementary and all single mismatched DNA targets. The terminally pyrenelabeled acpcPNA showed a much smaller fluorescence change upon hybridization with both complementary and mismatched DNA targets, and the change was in the opposite direction to the internally pyrene-labeled acpcPNA. These results were rationalized by the use of molecular dynamics simulations, which suggested that the pyrene label adopts a different conformation when located at different positions of the acpcPNA probes.
Tetrahedron, 2012
ABSTRACT Pyrene as well as other aromatic hydrocarbons could be successfully incorporated in to p... more ABSTRACT Pyrene as well as other aromatic hydrocarbons could be successfully incorporated in to pyrrolidinyl peptide nucleic acid bearing a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) as a base surrogate via a triazole linker employing Cu- catalyzed alkyne-azide cycloaddition (click chemistry). The labeling can be performed via a pre-clicked pyrene monomer or by post-synthetic modification of azide-containing acp cPNA on solid support. Thermal denaturation experiments suggested that the pyrene-triazole unit can be have as a universal base in the acpcPNA system. The mode of base-pairing has been proposed based on molecular dynamics simulations. Importantly, the fluorescence spectra of the pyrene-labeled single stranded acpcPNA and its hybrid with DNA are quite different. The ratio of emission s at 380 and 460 nm changed significantly (up to a factor of 7) upon hybrid formation with complementary DNA.
The Journal of Physical Chemistry B, 2008
Many key characteristics of hole transfer (HT) in DNA have been derived from spectroscopic studie... more Many key characteristics of hole transfer (HT) in DNA have been derived from spectroscopic studies of DNA hairpins. Because the capping groups in the hairpins can remarkably influence the structure and flexibility of the pi stack, and therefore, the charge transfer rate, the question arises of whether the HT parameters obtained for hairpins may be transferred to DNA oligomers. On the basis of large-time scale QM/MD simulations, we compare structural and electronic parameters of AT stacks in hairpins and DNA oligomers. We find that even in short hairpins, Sa-AA-Sd and Sa-AAA-Sd, the effects of the capping chromophores on the structure of the pi stack and the HT couplings properly averaged over MD trajectories are relatively small, and therefore, the hairpins are good models to study hole transfer through DNA. By contrast, the calculations of the electronic couplings based on the average structures of the systems lead to essential errors in the HT rate and the misleading statement that the charge transfer properties of DNA domains within hairpins are quite different from those of normal sequences.
The Journal of Physical Chemistry B, 2003
Solid State Sciences, 2013
Physical Chemistry Chemical Physics, 2001
Electronic matrix elements for hole transfer between adjacent WatsonCrick pairs in DNA have been... more Electronic matrix elements for hole transfer between adjacent WatsonCrick pairs in DNA have been calculated at the HartreeFock SCF level for various conformations of the dimer duplexes [(AT),(AT)],[(AT),(TA)],[(TA),(AT)]. Example configurations of [(TA),(TA)] have also ...
![Research paper thumbnail of Corrigendum to “Combined modification of zeolite NaY by phenyl trimethyl ammonium bromide and potassium for ethylene gas adsorption” [Microporous and Mesoporous Materials 153 (2012) 30–34]](https://attachments.academia-assets.com/44013316/thumbnails/1.jpg)
](Microporous and Mesoporous Materials, 2012
Journal of Thermal Analysis and Calorimetry, 2014
ABSTRACT The nickel phosphate octahydrate (Ni3(PO4)2·8H2O) was synthesized by a simple procedure ... more ABSTRACT The nickel phosphate octahydrate (Ni3(PO4)2·8H2O) was synthesized by a simple procedure and characterized by FTIR, TG/DTG/DTA, AAS, and XRD techniques. The morphologies of the title compound and its decomposition product were studied by the SEM method. The dehydration process of the synthesized hydrate occurred in one step over the temperature range of 120–250 °C, and the thermal decomposition product at 800 °C was found to be Ni3(PO4)2. The kinetic parameters (E and A) of this step were calculated using the Ozawa–Flynn–Wall and Kissinger–Akahira–Sunose methods. The iterative methods of both equations were carried out to determine the exact values of E, which confirm the single-step mechanism of the dehydration process. The non-isothermal kinetic method was used to determine the mechanism function of the dehydration, which indicates the contracting disk mechanism of R1 model as the most probable mechanism function and agrees well with the isothermal data. Besides, the isokinetic temperature value (T i) was calculated from the spectroscopic data. The thermodynamic functions of the activated complex (ΔS ≠, ΔH ≠, and ΔG ≠) of the dehydration process were calculated using the activated complex theory of Eyring. The kinetic parameters and thermodynamic functions of the activated complex for the dehydration process of Ni3(PO4)2·8H2O are reported for the first time.
Journal of Molecular Modeling, 2006
We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser... more We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser dyes pyronine 6G (P6G) and rhodamine 6G (R6G) in aqueous solution, generating trajectories of 2.5 ns for various computational protocols. We discuss how the choice of atomic partial charges and the length of the trajectories affect the predicted structures of the dimers and compare our results to those of earlier MD-simulations, which were restricted to only 0.7 ns. Our results confirm that monomers of P6G easily undergo relative rotations within the dimer, but we found new conformations of the R6G dimer at longer simulation times. In addition, we analyzed in detail the energy change during the formation of dimers. With suitable corrections, the electrostatic energy from an Ewald treatment agrees with the results from an approach relying on a residue-based cutoff. For P6G, we show that the strong solvent-mediated electrostatic attraction between the monomers is counteracted by an almost equally large solvent-induced entropy contribution to yield a small driving force to dimer formation, in very good agreement with the free-energy change from a thermodynamic-integration procedure. Thus, earlier rationalizations of the dimer formation, based only on energy arguments, yield a qualitatively wrong picture.
Inorganic Chemistry, 2011
Five new triply bridged dinuclear Cu(II) compounds have been synthesized, and their magnetic prop... more Five new triply bridged dinuclear Cu(II) compounds have been synthesized, and their magnetic properties have been measured and characterized. The magnetic coupling constants (J) of these compounds plus a previously structurally characterized compound of the same type have been derived by appropriate fitting of the experimentally measured molar susceptibility variation with the temperature. Two of the compounds are ferromagnetically coupled, and three are antiferromagnetically coupled with J values in the [+150, -40] cm(-1) range. The validity of the structural aggregate Addison's parameter as a qualitative magneto-structural correlation is confirmed. The origin of the magnetic interactions and the magnitude of the magnetic coupling have been analyzed by means of density functional theory-based calculations using a variety of state of the art exchange-correlation potentials. It is shown that the long-range separated LC-ωPBE provides the overall best agreement with experiment for this family as well as for a set of previously reported hetero triply bridged dinuclear Cu(II) compounds, especially for ferromagnetic systems.
Inorganic Chemistry, 2010
In the present work we present a comprehensive study of the magneto-structural correlations of a ... more In the present work we present a comprehensive study of the magneto-structural correlations of a series of ferromagnetic triply heterobridged Cu(II) dinuclear compounds containing [Cu(2)(mu-O(2)CR)(mu-OH)(mu-X)(L)(2)](2+) ions (where X = OH(2), Cl(-), OMe(-) and L = bpy, phen, dpyam) which have the particularity of being all ferromagnetic. The present theoretical study, based on hybrid density functional theory (DFT) calculations, leads to strong conclusions about the role of the pentacoordination geometry of the Cu(II) ions (square base pyramidal (SP) or trigonal bipyramidal (TBP) coordination) and the nature of the third bridging ligand in determining the final value of the magnetic coupling constants in this series of compounds. These investigations point toward the existence of a maximum value for the ferromagnetic interaction and may offer some useful information to synthetic chemists aiming at obtaining new compounds with enhanced ferromagnetism.
Chemical Physics Letters, 2013
ABSTRACT The structural properties and stability of two different stereoisomers of (1S,2S)-2-amin... more ABSTRACT The structural properties and stability of two different stereoisomers of (1S,2S)-2-aminocyclopentanecarboxylic acid (acpcPNA) binding to DNA and self hybrid DNA duplex were investigated using a molecular dynamics simulation. The thermodynamics stability was estimated and revealed that the stability of the simulated duplexes is of the order of (2‧R,4‧R)-acpcPNA·DNA > (2‧R,4‧S)-acpcPNA·DNA > DNA·DNA, which is in good agreement with experimental thermal stability. The lowest stability of DNA duplex is caused by a repulsion of two negatively charged backbones. The repulsion is decreased significantly by replacing a non-charged acpcPNA backbone, leading to a strong binding ability of acpcPNA with its complementary DNA.
Chemical Physics Letters, 2004
Biochemical and Biophysical Research Communications, 2008
Journal of Thermal Analysis and Calorimetry, 2015
ABSTRACT The olivine LiNiPO4 was synthesized via the calcination of the new precursor LiNiPO4·3H2... more ABSTRACT The olivine LiNiPO4 was synthesized via the calcination of the new precursor LiNiPO4·3H2O at 600 °C. The precursor was obtained from low-temperature (50 °C) wet chemical reaction. The results from XRD, FTIR, AAS/AES and TG/DTG/DTA techniques confirmed the formula of the title compounds. The SEM results indicated the morphologies of the hydrate precursor as thin plate particles and the calcined product as small bead particles. The BET surface area of the final calcined product at 600 °C is much higher (5.807 m2 g−1) than that reported in the literature (0.25 m2 g−1). The kinetic triplet [activation energy, E, pre-exponential factor, A, and the most probable mechanism function, g(α)] and the thermodynamic functions of activated complexes (ΔS ≠, ΔH ≠ and ΔG ≠) for the dehydration step of LiNiPO4·3H2O were determined and discussed. The mechanism of the dehydration process is the single-step A3/2 (assumed random nucleation and its subsequent growth). New information, namely the isobaric molar heat capacity, experimental entropy, enthalpy and Gibbs energy changes as function of temperature (K) of LiNiPO4·3H2O and LiNiPO4, was evaluated from the DSC data by third-order polynomial fitting and reported for the first time. The calculated corresponding thermodynamic functions from kinetic parameters are compared and discussed.
Inorganica Chimica Acta, 2011
Journal of Thermal Analysis and Calorimetry, 2015
ABSTRACT The olivine LiNiPO4 was synthesized via the calcination of the new precursor LiNiPO4·3H2... more ABSTRACT The olivine LiNiPO4 was synthesized via the calcination of the new precursor LiNiPO4·3H2O at 600 °C. The precursor was obtained from low-temperature (50 °C) wet chemical reaction. The results from XRD, FTIR, AAS/AES and TG/DTG/DTA techniques confirmed the formula of the title compounds. The SEM results indicated the morphologies of the hydrate precursor as thin plate particles and the calcined product as small bead particles. The BET surface area of the final calcined product at 600 °C is much higher (5.807 m2 g−1) than that reported in the literature (0.25 m2 g−1). The kinetic triplet [activation energy, E, pre-exponential factor, A, and the most probable mechanism function, g(α)] and the thermodynamic functions of activated complexes (ΔS ≠, ΔH ≠ and ΔG ≠) for the dehydration step of LiNiPO4·3H2O were determined and discussed. The mechanism of the dehydration process is the single-step A3/2 (assumed random nucleation and its subsequent growth). New information, namely the isobaric molar heat capacity, experimental entropy, enthalpy and Gibbs energy changes as function of temperature (K) of LiNiPO4·3H2O and LiNiPO4, was evaluated from the DSC data by third-order polynomial fitting and reported for the first time. The calculated corresponding thermodynamic functions from kinetic parameters are compared and discussed.
The Journal of Physical Chemistry Letters, 2015
Molecular structures that direct charge transport in two or three dimensions possess some of the ... more Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among "well stacked" conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups ("extenders") lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA.
The Journal of Physical Chemistry C, 2010
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2012
ABSTRACT During the last two decades, electron transfer (ET) through DNA and its artificial analo... more ABSTRACT During the last two decades, electron transfer (ET) through DNA and its artificial analogues has been an area of extensive experimental and theoretical studies. This process plays an important role in biology (damage and repair of DNA in living cells) and is of potential interest in material sciences. Because structural dynamics of the π stack and its environment affect essentially the electron transport, some significant details of excess charge migration cannot be derived from experiments. Computer simulations of the ET process provide microscopic insights into mechanisms of this process. In the paper, we consider computational methods used to describe the propagation of excess charges through π stacks of DNA and related systems. © 2012 John Wiley & Sons, Ltd.
RSC Advances, 2014
ABSTRACT Nucleic acids or nucleic acid analogues carrying an environment sensitive fluorophore th... more ABSTRACT Nucleic acids or nucleic acid analogues carrying an environment sensitive fluorophore that can change optical properties in response to hybridization with complementary DNA or RNA targets are potentially useful as self-reporting hybridization probes that do not require a quencher. In this study, pyrrolidinyl peptide nucleic acids (acpcPNA) carrying a pyrene label at terminal, or internal positions were synthesized and their fluorescence properties investigated. Significant fluorescence increases, between 2.9 and 73 fold, were observed only with internally pyrene-labeled acpcPNA upon hybridization with complementary DNA under a variety of sequence contexts. Hybridization with mismatched DNA targets yielded mostly unchanged or decreased fluorescence, depending on the type and position of the mismatch base. Non-specific fluorescence increase due to the presence of a mismatch located away from the pyrene label could be eliminated by digestion with S1 nuclease, which allows unambiguous discrimination between complementary and all single mismatched DNA targets. The terminally pyrenelabeled acpcPNA showed a much smaller fluorescence change upon hybridization with both complementary and mismatched DNA targets, and the change was in the opposite direction to the internally pyrene-labeled acpcPNA. These results were rationalized by the use of molecular dynamics simulations, which suggested that the pyrene label adopts a different conformation when located at different positions of the acpcPNA probes.
Tetrahedron, 2012
ABSTRACT Pyrene as well as other aromatic hydrocarbons could be successfully incorporated in to p... more ABSTRACT Pyrene as well as other aromatic hydrocarbons could be successfully incorporated in to pyrrolidinyl peptide nucleic acid bearing a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) as a base surrogate via a triazole linker employing Cu- catalyzed alkyne-azide cycloaddition (click chemistry). The labeling can be performed via a pre-clicked pyrene monomer or by post-synthetic modification of azide-containing acp cPNA on solid support. Thermal denaturation experiments suggested that the pyrene-triazole unit can be have as a universal base in the acpcPNA system. The mode of base-pairing has been proposed based on molecular dynamics simulations. Importantly, the fluorescence spectra of the pyrene-labeled single stranded acpcPNA and its hybrid with DNA are quite different. The ratio of emission s at 380 and 460 nm changed significantly (up to a factor of 7) upon hybrid formation with complementary DNA.
The Journal of Physical Chemistry B, 2008
Many key characteristics of hole transfer (HT) in DNA have been derived from spectroscopic studie... more Many key characteristics of hole transfer (HT) in DNA have been derived from spectroscopic studies of DNA hairpins. Because the capping groups in the hairpins can remarkably influence the structure and flexibility of the pi stack, and therefore, the charge transfer rate, the question arises of whether the HT parameters obtained for hairpins may be transferred to DNA oligomers. On the basis of large-time scale QM/MD simulations, we compare structural and electronic parameters of AT stacks in hairpins and DNA oligomers. We find that even in short hairpins, Sa-AA-Sd and Sa-AAA-Sd, the effects of the capping chromophores on the structure of the pi stack and the HT couplings properly averaged over MD trajectories are relatively small, and therefore, the hairpins are good models to study hole transfer through DNA. By contrast, the calculations of the electronic couplings based on the average structures of the systems lead to essential errors in the HT rate and the misleading statement that the charge transfer properties of DNA domains within hairpins are quite different from those of normal sequences.
The Journal of Physical Chemistry B, 2003
Solid State Sciences, 2013
Physical Chemistry Chemical Physics, 2001
Electronic matrix elements for hole transfer between adjacent WatsonCrick pairs in DNA have been... more Electronic matrix elements for hole transfer between adjacent WatsonCrick pairs in DNA have been calculated at the HartreeFock SCF level for various conformations of the dimer duplexes [(AT),(AT)],[(AT),(TA)],[(TA),(AT)]. Example configurations of [(TA),(TA)] have also ...
Microporous and Mesoporous Materials, 2012
Journal of Thermal Analysis and Calorimetry, 2014
ABSTRACT The nickel phosphate octahydrate (Ni3(PO4)2·8H2O) was synthesized by a simple procedure ... more ABSTRACT The nickel phosphate octahydrate (Ni3(PO4)2·8H2O) was synthesized by a simple procedure and characterized by FTIR, TG/DTG/DTA, AAS, and XRD techniques. The morphologies of the title compound and its decomposition product were studied by the SEM method. The dehydration process of the synthesized hydrate occurred in one step over the temperature range of 120–250 °C, and the thermal decomposition product at 800 °C was found to be Ni3(PO4)2. The kinetic parameters (E and A) of this step were calculated using the Ozawa–Flynn–Wall and Kissinger–Akahira–Sunose methods. The iterative methods of both equations were carried out to determine the exact values of E, which confirm the single-step mechanism of the dehydration process. The non-isothermal kinetic method was used to determine the mechanism function of the dehydration, which indicates the contracting disk mechanism of R1 model as the most probable mechanism function and agrees well with the isothermal data. Besides, the isokinetic temperature value (T i) was calculated from the spectroscopic data. The thermodynamic functions of the activated complex (ΔS ≠, ΔH ≠, and ΔG ≠) of the dehydration process were calculated using the activated complex theory of Eyring. The kinetic parameters and thermodynamic functions of the activated complex for the dehydration process of Ni3(PO4)2·8H2O are reported for the first time.
Journal of Molecular Modeling, 2006
We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser... more We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser dyes pyronine 6G (P6G) and rhodamine 6G (R6G) in aqueous solution, generating trajectories of 2.5 ns for various computational protocols. We discuss how the choice of atomic partial charges and the length of the trajectories affect the predicted structures of the dimers and compare our results to those of earlier MD-simulations, which were restricted to only 0.7 ns. Our results confirm that monomers of P6G easily undergo relative rotations within the dimer, but we found new conformations of the R6G dimer at longer simulation times. In addition, we analyzed in detail the energy change during the formation of dimers. With suitable corrections, the electrostatic energy from an Ewald treatment agrees with the results from an approach relying on a residue-based cutoff. For P6G, we show that the strong solvent-mediated electrostatic attraction between the monomers is counteracted by an almost equally large solvent-induced entropy contribution to yield a small driving force to dimer formation, in very good agreement with the free-energy change from a thermodynamic-integration procedure. Thus, earlier rationalizations of the dimer formation, based only on energy arguments, yield a qualitatively wrong picture.
Inorganic Chemistry, 2011
Five new triply bridged dinuclear Cu(II) compounds have been synthesized, and their magnetic prop... more Five new triply bridged dinuclear Cu(II) compounds have been synthesized, and their magnetic properties have been measured and characterized. The magnetic coupling constants (J) of these compounds plus a previously structurally characterized compound of the same type have been derived by appropriate fitting of the experimentally measured molar susceptibility variation with the temperature. Two of the compounds are ferromagnetically coupled, and three are antiferromagnetically coupled with J values in the [+150, -40] cm(-1) range. The validity of the structural aggregate Addison's parameter as a qualitative magneto-structural correlation is confirmed. The origin of the magnetic interactions and the magnitude of the magnetic coupling have been analyzed by means of density functional theory-based calculations using a variety of state of the art exchange-correlation potentials. It is shown that the long-range separated LC-ωPBE provides the overall best agreement with experiment for this family as well as for a set of previously reported hetero triply bridged dinuclear Cu(II) compounds, especially for ferromagnetic systems.
Inorganic Chemistry, 2010
In the present work we present a comprehensive study of the magneto-structural correlations of a ... more In the present work we present a comprehensive study of the magneto-structural correlations of a series of ferromagnetic triply heterobridged Cu(II) dinuclear compounds containing [Cu(2)(mu-O(2)CR)(mu-OH)(mu-X)(L)(2)](2+) ions (where X = OH(2), Cl(-), OMe(-) and L = bpy, phen, dpyam) which have the particularity of being all ferromagnetic. The present theoretical study, based on hybrid density functional theory (DFT) calculations, leads to strong conclusions about the role of the pentacoordination geometry of the Cu(II) ions (square base pyramidal (SP) or trigonal bipyramidal (TBP) coordination) and the nature of the third bridging ligand in determining the final value of the magnetic coupling constants in this series of compounds. These investigations point toward the existence of a maximum value for the ferromagnetic interaction and may offer some useful information to synthetic chemists aiming at obtaining new compounds with enhanced ferromagnetism.
Chemical Physics Letters, 2013
ABSTRACT The structural properties and stability of two different stereoisomers of (1S,2S)-2-amin... more ABSTRACT The structural properties and stability of two different stereoisomers of (1S,2S)-2-aminocyclopentanecarboxylic acid (acpcPNA) binding to DNA and self hybrid DNA duplex were investigated using a molecular dynamics simulation. The thermodynamics stability was estimated and revealed that the stability of the simulated duplexes is of the order of (2‧R,4‧R)-acpcPNA·DNA > (2‧R,4‧S)-acpcPNA·DNA > DNA·DNA, which is in good agreement with experimental thermal stability. The lowest stability of DNA duplex is caused by a repulsion of two negatively charged backbones. The repulsion is decreased significantly by replacing a non-charged acpcPNA backbone, leading to a strong binding ability of acpcPNA with its complementary DNA.
Chemical Physics Letters, 2004
Biochemical and Biophysical Research Communications, 2008