This document discusses cisplatin, an anticancer drug. It summarizes computational studies examining the effects of substituting different ligands on cisplatin's central platinum atom. Bond lengths, angles, and electrostatic charges were calculated. Iodine substitution caused the greatest increase in bond length due to iodine's large size. Bromine substitution most affected bond angles. More electronegative ligands led to more positive charges on the platinum atom. In general, larger and less electronegative ligands had greater effects on geometry and charge distribution compared to the original cisplatin molecule.
Hyperconjugation is the donation of a sigma bond into an adjacent empty or partially filled p orbital, which results in an increased stability of the molecule.
Contributed by: Samuel Redstone (Undergraduate), University of Utah, 2016
A Suspected Derivative Morphology for pheophytin (脫鎂葉綠素) and the Enhanced H...cclarbl
● What’s the role of pheophytin (pheo) in photosynthesis?
● What might be pheo’s other structure-related roles? → things we bumped into in the original low-power chlorophyll battery
●. Porphyrin-ring family and their uses
●. A conjectured derivative morphology and associated proton conduction path within pheophytins (pheo’s)
● Spectral comparison among: 1st-principle quantum simulation, measurement on ethanol-extracted pheo, and existing literature
● Experimental evidence in pheo-catalyzed decomposition of hydrogen gas
● Summary and conclusions
Hyperconjugation is the donation of a sigma bond into an adjacent empty or partially filled p orbital, which results in an increased stability of the molecule.
Contributed by: Samuel Redstone (Undergraduate), University of Utah, 2016
A Suspected Derivative Morphology for pheophytin (脫鎂葉綠素) and the Enhanced H...cclarbl
● What’s the role of pheophytin (pheo) in photosynthesis?
● What might be pheo’s other structure-related roles? → things we bumped into in the original low-power chlorophyll battery
●. Porphyrin-ring family and their uses
●. A conjectured derivative morphology and associated proton conduction path within pheophytins (pheo’s)
● Spectral comparison among: 1st-principle quantum simulation, measurement on ethanol-extracted pheo, and existing literature
● Experimental evidence in pheo-catalyzed decomposition of hydrogen gas
● Summary and conclusions
Organic Reaction Mechanism : This topic is very-very important for CSIR-NET, GATE, IIT-JAM and other Competitive exams for Chemistry and Chemical Sciences.
Superconductivity in Al-substituted Ba8Si46 clathratesYang Li
There is a great deal of interest vested in the superconductivity of Si clathrate compounds with sp3 network, in which the structure is dominated by strong covalent bonds among silicon atoms, rather than the metallic bonding that is more typical of traditional superconductors. A joint experimental and theoretical investigation of superconductivity in Al-substituted type-I silicon clathrates is reported. Samples of the general formula Ba8Si46xAlx, with different values of x were prepared. With an increase in the Al composition, the superconducting transition temperature TC was observed to decrease systematically. The resistivity measurement revealed
that Ba8Si42Al4 is superconductive with transition temperature at TC=5.5 K. The magnetic measurements showed that the bulk superconducting Ba8Si42Al4 is a type II superconductor. For x=6 sample Ba8Si40Al6, the superconducting transition was observed down to TC=4.7K which pointed to a strong suppression of superconductivity with increasing Al content as compared with TC=8K for Ba8Si46. Suppression of superconductivity can be attributed primarily to a
decrease in the density of states at the Fermi level, caused by reduced integrity of the sp3 hybridized networks as well as the lowering of carrier concentration. These results corroborated
by first-principles calculations showed that Al substitution results in a large decrease of the electronic density of states at the Fermi level, which also explains the decreased superconducting critical temperature within the BCS framework. The work provided a comprehensiveunderstanding of the doping effect on superconductivity of clathrates.
Formation of Porphyrin Nanowires via Beta-Cyclodextrin-Adamantane Host-Guest ...Logan Fenimore
-Employed principles of supramolecular chemistry and manipulated fluorescence, chelation, and reactive properties of porphyrin molecules to form nanowires in solution for therapeutic and drug delivery purposes
-Studied host-guest binding interactions between β-cyclodextrin and adamantane functional groups in order to minimize molecular aggregation of porphyrins and promote solubility of inclusion complexes in water
-Mastered thin-layer and column chromatography and liquid-liquid extractions to separate and purify product mixtures of porphyrin synthetic scheme
-Used electrospray ionization (ESI) and matrix assisted laser desorption ionization - time of flight (MALDI-TOF) mass spectrometry, proton nuclear magnetic resonance (NMR), scanning electron microscopy (SEM), and ultraviolet-visible (UV-Vis) absorption spectroscopy and respective instruments to characterize products and intermediates of porphyrin synthetic scheme
-Presented attached poster named "Formation of Porphyrin Nanowires via β-Cyclodextrin-Adamantane Host-Guest Binding" at SMART REU Closing Symposium
Introduction
working principle
fragmentation process
general rules for fragmentation
general modes of fragmentation
metastable ions
isotopic peaks
applications
This powerpoint presentation will cover following aspects:
Kinds of Pericyclic Reactions and Brief details of their kinds
Molecular Orbitals and Orbitals Symmetry
Molecular Orbitals Description
Electrocyclic Reactions
Introduction to Dienes
Introduction to Dienophiles
Photochemical conditions
Ring Closure
Modes of Ring Closure
Diels- Alder Product recognition and Reversibility of Diels Alder Reaction
Conrotatory and Disrotatory arrangements
Cycloadditions in Complete Details
Dimerization , Frontier Orbitals Description, Endo Rule, Stereochemistry, Applications Hoffman's rule and a lot more……
Analystik développement logiciels à forfaitAnalystik
Analystik a développé une grande expertise dans le développement d’applications et de systèmes informatiques, particulièrement pour le monde de la finance. Plusieurs grandes banques canadiennes sont nos clients, mais aussi d’autres grands noms comme Cascades et Bombardier.
Organic Reaction Mechanism : This topic is very-very important for CSIR-NET, GATE, IIT-JAM and other Competitive exams for Chemistry and Chemical Sciences.
Superconductivity in Al-substituted Ba8Si46 clathratesYang Li
There is a great deal of interest vested in the superconductivity of Si clathrate compounds with sp3 network, in which the structure is dominated by strong covalent bonds among silicon atoms, rather than the metallic bonding that is more typical of traditional superconductors. A joint experimental and theoretical investigation of superconductivity in Al-substituted type-I silicon clathrates is reported. Samples of the general formula Ba8Si46xAlx, with different values of x were prepared. With an increase in the Al composition, the superconducting transition temperature TC was observed to decrease systematically. The resistivity measurement revealed
that Ba8Si42Al4 is superconductive with transition temperature at TC=5.5 K. The magnetic measurements showed that the bulk superconducting Ba8Si42Al4 is a type II superconductor. For x=6 sample Ba8Si40Al6, the superconducting transition was observed down to TC=4.7K which pointed to a strong suppression of superconductivity with increasing Al content as compared with TC=8K for Ba8Si46. Suppression of superconductivity can be attributed primarily to a
decrease in the density of states at the Fermi level, caused by reduced integrity of the sp3 hybridized networks as well as the lowering of carrier concentration. These results corroborated
by first-principles calculations showed that Al substitution results in a large decrease of the electronic density of states at the Fermi level, which also explains the decreased superconducting critical temperature within the BCS framework. The work provided a comprehensiveunderstanding of the doping effect on superconductivity of clathrates.
Formation of Porphyrin Nanowires via Beta-Cyclodextrin-Adamantane Host-Guest ...Logan Fenimore
-Employed principles of supramolecular chemistry and manipulated fluorescence, chelation, and reactive properties of porphyrin molecules to form nanowires in solution for therapeutic and drug delivery purposes
-Studied host-guest binding interactions between β-cyclodextrin and adamantane functional groups in order to minimize molecular aggregation of porphyrins and promote solubility of inclusion complexes in water
-Mastered thin-layer and column chromatography and liquid-liquid extractions to separate and purify product mixtures of porphyrin synthetic scheme
-Used electrospray ionization (ESI) and matrix assisted laser desorption ionization - time of flight (MALDI-TOF) mass spectrometry, proton nuclear magnetic resonance (NMR), scanning electron microscopy (SEM), and ultraviolet-visible (UV-Vis) absorption spectroscopy and respective instruments to characterize products and intermediates of porphyrin synthetic scheme
-Presented attached poster named "Formation of Porphyrin Nanowires via β-Cyclodextrin-Adamantane Host-Guest Binding" at SMART REU Closing Symposium
Introduction
working principle
fragmentation process
general rules for fragmentation
general modes of fragmentation
metastable ions
isotopic peaks
applications
This powerpoint presentation will cover following aspects:
Kinds of Pericyclic Reactions and Brief details of their kinds
Molecular Orbitals and Orbitals Symmetry
Molecular Orbitals Description
Electrocyclic Reactions
Introduction to Dienes
Introduction to Dienophiles
Photochemical conditions
Ring Closure
Modes of Ring Closure
Diels- Alder Product recognition and Reversibility of Diels Alder Reaction
Conrotatory and Disrotatory arrangements
Cycloadditions in Complete Details
Dimerization , Frontier Orbitals Description, Endo Rule, Stereochemistry, Applications Hoffman's rule and a lot more……
Analystik développement logiciels à forfaitAnalystik
Analystik a développé une grande expertise dans le développement d’applications et de systèmes informatiques, particulièrement pour le monde de la finance. Plusieurs grandes banques canadiennes sont nos clients, mais aussi d’autres grands noms comme Cascades et Bombardier.
Conocer al cliente es un factor clave para llegar a el con productos de valor, la diferencia de un producto con respecto a su comcpetencia en muchos casos, meramente conceptual y solo sabiendo profundamente qué es lo que persive nuestro cliente como valioso podemos llegar a él de forma efectiva
Tools for target identification and validationDr. sreeremya S
Microarrays
Target identification seeks to identify new targets, normally
proteins (or DNA/RNA), whose modulation might
inhibit or reverse disease progression. Current technologies
enable researchers to attempt to correlate changes in
gene (genomics) and protein (proteomics) expression
with human disease, in the hope of finding new targets.
Microarrays are a well-utilized tool in both academic and
industrial research laboratories. They can be used to
assess gene and protein expression (via nucleic acid or
protein microarrays) to identify novel targets, and can also
be used to validate the found targets at the tissue or cell
scale (via tissue or cell microarrays
Non covalent interactions are incredibly important characteristics in supermolecular chemistry, especially in biological molecules, such as nucleic acids and enzymes. These can include pi-pi, pi-cation and electrostatic interactions.
Contributed by:
Alexandra Kent & Allyson Brome (Undergraduate Students)
University of Utah
2014
• Background and motivation – the success of pheophytin (pheo, 脫鎂葉綠素) catalyst
• Porphyrin-ring family and roles of their derivative morphologies
• Similar derivatives within DNA base pairs
• 1st-principle simulation of simplified H2 decomposition steps involving derivative DNA base pairs à energetically favorable?
• Wet DNA-catalyzed chemical battery experiment and result
• Dry DNA-catalyzed hydrogen fuel cell under room temperature
• Summary and conclusions
A Remarkable Conflict Between Biochemical Dogma And Radical Concept :
Traditional Concept :
By the 1950s it had been clearly established that oxidative phosphorylation involved the stepwise transfer of electrons through a series of carriers to molecular oxygen. But how the energy derived from these electron transfer reactions was converted to ATP remained a mystery. The general assumption was that ADP was converted to ATP by direct transfer of high-energy phosphate groups from some other intermediate. Thus it was postulated that high-energy intermediates were produced as a result of electron transfer reactions and that these intermediates drove ATP synthesis by phosphate group transfer.
Concept Proposed By Peter Mitchell :
The fundamental proposal of the chemiosmotic hypothesis was that the “intermediate” that coupled electron transport to ATP synthesis was a proton electrochemical gradient across the membrane. Mitchell postulated that such a gradient was produced by electron transport and that the flow of protons back across the membrane in the energetically favorable direction was then coupled to ATP synthesis
1. Cisplatin
ABSTRACT:
Since the discovery of anti cancer activity of Cisplatin, it has enjoyed a huge proclamation and clinical hit.
In this report using Spartan `10 V1.1.0 Molecular mechanics and Hartee-Fock calculations have been performed
using different substituent on the central Platinum atom, substituent like F, Cl, Br, I, NH2, OH are used for studying
energy and geometrics. The parameters like bond length, bond angle, electrostatic charge, dipole moment, Energy
have been compared. The deviation in the bond length from the original molecule is observed greatest with iodine;
this might be due to the larger size. Further bond angle calculations have been performed; the most affected is the
bromine substituted; this might be due to the higher electronegativity. The electrostatic charge studies showed that
with the increase in charge of the substituent atom, the electro positive charge on the central metal atom kept
increasing. Dipole moment calculations showed that, when –OH group –NH3group is substituted it displayed
relatively lower dipole moment which interpreted the molecule is much more stable, than when iodine is substituted
which has relatively a much larger dipole moment.
INTRODUCTION:
Cancer is one of the most common
diseases in the world; it has also
become the most important cause
of deaths in recent years1
. The use
of metals in curing diseases can be
traced back almost 5000 years.
Transitional metal complexes are
nowadays used as alkylating
agents in the treatment of cancer.
The development of the
coordinating chemistry has
revolutionized and facilitated
chemists using metals
centers for synthesizing
coordinating complex
molecules as drugs, metal centers
being positively charged are able
to bind to the negatively charged
biomolecules2
.
Cisplatin is one those
complex molecule which has a
platinum center, it was only in
mid 1960`s when anticancer
activity of Cisplatin was
discovered. Cisplatin is believed
to exert its anticancer effect by
interacting with DNA, inducing
programmed cell death. Cisplatin
and its analogues interacts with
the purine base pairs in the DNA;
forming DNA-Pt (NH3)2-DNA,
which inhibits DNA replication
and ultimate cell death3
.
Cisplatin is a metallic
coordinating complex, molecular
formula is (NH3)2PtCl2. It has a
molecular weight of 300gm/mol.
It has square planar geometry. It is
white or deep yellow to yellow-
orange crystalline powder at room
temperature4
.
Fig 1: Structure of Cisplatin
2. Cisplatin
Cisplatin can be prepared by using
Potassium
tetracholoroplatinate(II), the first
NH3 ligand can be added at any
position the second one is added
to cis or trans to the bound amine
ligand5
. Further investigation with
this drug is complicated mode of
action of the drug.6
Cisplatin has –NH3 groups
attached to the central Platinum
metal atom, the bond distance
from Pt-Cl measure 2.5A, where
as the bond distance between Pt-
NH3 is 2.1A. The electro
negativity of Cl and N is 3.0, so
the charge is symmetrically
distributed, due to which the
molecule is slight soluble in water.
Table 1: Physicochemical properties
of Cisplatin
Property Data
Molecular Formula H6Cl2N2Pt
Molecular weight 300.1g/mol
Physical State Crystalline powder
Molecular Shape Square planar
Solubility Slightly soluble in
water, soluble in
dimethylprimanide
and N,N-
dimethylfor
mamide
Density 3.74gm/m3
Stability Transforms to
trans over time
2. MECHANISM OF ACTION:
Cancer can be considered a failure
of cell to undergo apoptosis. In
norma cells, sensors to cell
abnormalities lead to withdrawal
of survival signals, there by
leading to cell death7
. In Cisplatin,
it induces cell death of cancer cell
by interacting with the DNA
synthesis. The platinum atom
binds to the DNA base pairs; cross
linking of the complex occurs
when chloride ligand is displaced.
By this way several cross linking
occurs there by interfering with
the cell division, which in turn
activates apoptosis8-9
.
3. EXPERIMENTAL SECTION:
3.1 Computational Methods:
The present study on the
Cisplatin molecule is completely
theoretical. Using Spartan `10
V1.1.0 the theoretical studies have
been carried out on a high
performance computer. The
calculations that are carried out
include Molecular mechanics and
Hartree-Fock. The Equilibrium
Geometry studied with Hartree-
Fock is studied under 6-31G*. The
other calculations include simpler
findings like Bond Angle, Bond
3. Cisplatin
Length data and charges on the
atoms are calculated.
Further Calculations are
done by changing the ligands on
the central atom; atoms which are
more electronegative and also less
electronegative than the parent
molecule have been studied, along
with other ligands.
4. RESULTS AND
DISCUSSION:
Different forms of Cisplatin are
formed by substituting the –Cl
with different electron donating
groups and electron withdrawing
groups. The affect on the bond
length and bond angle have been
observed.
Fig. 2. Cisplatin and other substituted
forms of cisplatin
4.1 Molecular Mechanics
The Cisplatin molecule which
contains two chlorines, the
chlorines are substituted with
different halogens, hydroxyl group
and NH3 group and the bond
distance, bond angle and the
charge on the molecule is found
out. For calculating the mentioned
parameters Spartan `10 V1.1.0
have been used.
4.1.1 Bond Lengths
Bond length or bond distance is
the average distance between
nuclei of two bonded atoms in a
molecule.
Table 2: Bond length parameter
of Cisplatin and its substituent
In the above table the
values of bond angle for the
different substituted groups on the
platinum center of Cisplatin,
which is studied with hartree-Fock
set.
Substituent Bond Angle in Ao
Pt-
Substituted
N-H Pt-N O-H
-F 1.90 1.00 1.85 -
-Br 2.48 1.00 2.13 -
-I 2.70 1.01 2.10 -
-OH 2.10 1.01 1.98 0.958
-NH3 2.10 1.01 2.10
-Cl 2.63 1.08 2.12 -
4. Cisplatin
4.1.2 Bond Angle and
Electrostatic Charge
From the results obtained in the
table 2, it can be interpreted that
the change in the bond length due
to various substituent. The most
deviation from the original value
of bond length is observed with
iodine, this is due to the large size
of the iodine molecule
Table3:Hartree-Fockoptimizedbondanglesforcisplatin
BondAngles
N2H5H6
35.26
35.26
35.26
35.26
35.26
35.26
H4N2H5
109.47
109.47
107.95
109.47
109.47
109.47
N1H2H3
35.26
35.26
35.26
35.26
35.26
35.26
N1H1H3
35.26
35.26
35.26
35.26
35.26
35.26
N1PtN2
75.36
45
43.23
90
90
90
suPtN
90
90
85.57
90
90
90
su,Pt,su
90
90
95.36
90
90
90
Substitu
F
Cl
Br
I
OH
NH3
The results obtained from
the table 3 indicate that, the
various changes that occurs in the
bond angle due to substitution of
various group on the central metal
atom. The most deviated result
obtained is the substitution of
fluorine, due to its high
electronegativity the bond angle is
constrained. Another deviation
observed in the substitution of
Bromine, due to the large size of
bromine the bond angle changes.
From the table 4, the
results obtained showed
electrostatic charge which varies
according to the change in the
substituent group; with the
decrease in electronegativity on
the substituent group the positive
charge on the central atom
increase. Fluorine is the most
electronegative group; fluorine
substitution has lowest positive
charge on the central atom when
compared to the least negative
group Iodine; which shows
highest positive charge on the
central metal atom.
Fluorine is the most
electronegative atom; it pulls the
electron density from the adjacent
metal atom there by leaving least
positive charge on the central
metal atom when compared to the
lesser electronegative atom than
fluorine
5. Cisplatin
Table4.Hartree-FockStabalizedElectrostaticchargeoncisplatinanditssubstituents
N2
-2.46
-3.48
-3.88
-24.41
N1
-2.46
-3.48
-3.88
-24.41
Charge
Pt
49.66
52.44
53.39
312.26
Sub
-5.56
-13.14
-15.13
-148.2
Sub
-5.56
-13.14
-15.13
-148.2
Subs
F
Cl
Br
I
5. CONCLUSION:
From the Hartree-Fock and
molecular mechanics calculations
its is observed that there is a much
larger deviation in the iodine
substituted Cisplatin, this is
probably due to the larger size and
lower electronegativity of iodine
when compared to chlorine in the
original molecule. In the
calculation related to bond angle,
the bond angle increases with the
increase in the size of the
substituent group; in this very
particular case; the increase in
bond angle is subjected to increase
with electron donating group.
The study related to the
electrostatic charge; the charge on
the central atom increases with the
decrease in the electronegativity
and size of the substituent group,
fluorine which is the most
electronegative atom substituted
made the central atom positive by
drawing electron towards itself;
there by developing a positive
charge on the central atom
5.1 Note
The study done through this paper
is theoretical work. The affect of
the Cisplatin drug or its
substituent on the human body or
stimulated system is not known.
6. ACKNOWLEDGEMENTS:
I would like to thank Dr. Allan D.
Headley and for giving me this
opportunity to work on this
software and for their assistance.
7. REFERENCES:
6. Cisplatin
[1] Cornel Baltă, $icoleta G. Hădărugă1,
Carmen Manuela Plesa (Mitar), Daniel Ghibu,
Gabriela Garban, Zeno Garban, Daniel I.
Hădărugă (2012).Hematological properties of
cisplatin and its Ficaria verna Huds. extracts /
β-cyclodextrin complexes in rats, Journal of
Agroalimentary Processes and Technologies
2012, 18 (4), 356-359
[2] Irena Kostova,(2006), Platinium
complexes as anti cancer agents, Recent
patents on anti cancer drug discovery, 2006,
1, 1-22
[3] Rebecca A.Alderden, Matthew D.Hall, and
Trevor W.Hambley (2006), The discovery and
development of Cisplatin, Journal of Chemical
Education, 2006, Vol 83, No 5.
[4] P. J. Gee a & W. F. van Gunsteren,(2011)
Report on Carcinogens, National Toxicology
program 2011, Vol 12.
[5] Alderen RA, Hall MD, Hambley TW (2006),
Discovery and development of Cisplatin,
Journal of Chem Ed. Vol 83 (5) 728-724
[6] DF Long and AJ Repta (1981), Cisplatin:
Chemistry, distribution and
biotransformation 1981, Biopharmaceutics
and Drug dipostion, VOl 2, 1-16
[7] Wilson and Gisvold, Organic medicinal
and pharmaceutical chemistry, 12th
edition,
Philadelphia. PA 2004.
[8] Stephen Trzaska (2005); Cisplatin; C&EN
News Vol 83, 25
[9] Pruefer FG, Lizarraga F, Maldonado V,
Melendez-Zajgla J ( 2008). "Participation of
Omi Htra2 serine-protease activity in the
apoptosis induced by cisplatin on SW480
colon cancer cells". J Chemother 20 (3): 348–
54
_____________________________________
__________
COMPUTATIONAL STUDIES ON THE
ANTI- NEOPLASTIC AGENT
7. Cisplatin
“CISPLATIN” AND ITS SUBSTITUENT
USING SPARTAN `10
- Syed Zia ul Quasim, Dr. Allan D Headley
- Department of chemistry, Texas A&M University -
Commerce, Texas 2013 USA.