Publications (47)63.13 Total impact
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Article: Nature of π-Interactions in Nitrogen-Containing Heterocyclic Systems: A Structural Database Analysis
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ABSTRACT: Noncovalent interactions involving heteroaromatic ring systems play a major role in determining the function of many chemical as well as biological molecules. Therefore, detailed quantitative analyses of the π-interactions (X−H···π and π···π) were carried out for nitrogen-containing π-systems (isoxazole, imidazole, and indole moieties). Statistical analysis of the geometrical properties for the oxygen, nitrogen, and carbon atom donors with the heterocyclic π-system acceptors showed that carbon donors participate in relatively large numbers for X−H···π interactions, and they adopt T-shaped geometry. The π···π interaction analysis was categorized into three types based on the involvement of the heterocyclic π-systems with themselves, with any other benzene ring present in that particular structure, and their influence on the formation of π-interactions between benzene−benzene rings found in that particular compound. The π-systems in all the three categories prefer to form offset stacking π···π interaction geometry. The benzene rings which normally favor the formation of T-shaped geometry are found to prefer offset stacking geometry, which may be due to the influence of the heteroatom. The π-systems in these heterocyclic structures behave similar to the phenylalanine−phenylalanine interactions in proteins, and therefore this quantitative analysis can serve as a guide for structural and biological studies.01/2006; -
Article: Crystal structure and conformation study of N‐methyl‐t‐3‐methyl‐r‐2, c‐6‐diphenylpiperidin‐4‐one thiosemicarbazone
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ABSTRACT: Thiosemicarbazones are having the ability to bind with metal and inhibit the enzyme ribonucleoside diphosphate reductase (RDR), an enzyme which is involved in the synthesis of DNA precursors in the mammalian cells. The title compound N-methyl-t-3-methyl-r-2, c-6-diphenylpiperidin-4-one thiosemicarbazone (NMMDPT), CCDC 218052, was prepared using Mannich reaction and characterized by X-ray diffraction methods. The crystal data are: C20H24N4S; M.W = 352.49, triclinic, space group P, a = 8.467(2) Å, b = 10.228(2) Å, c = 12.249(2) Å; = 92.595(3)°, β = 104.173(3)°, =113.628(3)°; V = 930.0(3) Å3, Z = 2, Dcal = 1.259 Mgm–3, µ = 0.184 mm–1, λ (MoK)= 0.71073 Å, final R1 and wR2 are 0.0470 and 0.1052, respectively. The piperidine rings adopt chair conformation. The planar phenyl rings are oriented equatorially at 2,6-positions of the piperidine ring. The molecular packing can be viewed as dimers held together by two N–H…S types of intermolecular hydrogen bonds. Weak C–H…π interactions also support the stability of the molecules in the crystal in addition to van der Waals forces. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)Crystal Research and Technology 01/2006; 41(2):192 - 197. · 0.95 Impact Factor -
Article: Importance of main-chain hydrophobic free energy to the stability of thermophilic proteins.
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ABSTRACT: Living organisms are found in the most unexpected places, including deep-sea vents at 100 degrees C and several hundred bars pressure, in hot springs. Needless to say, the proteins found in thermophilic species are much more stable than their mesophilic counterparts. There are no obvious reasons to say that one would be more stable than others. Even examination of the amino acids and comparison of structural features of thermophiles with mesophilies cannot bring satisfactory explanation for the thermal stability of such proteins. In order to bring out the hidden information behind the thermal stabilization of such proteins in terms of energy factors and their combinations, analysis were made on good resolution structures of thermophilic and their mesophilic homologous from 23 different families. From the structural coordinates, free energy contributions due to hydrophobic, electrostatic, hydrogen bonding, disulfide bonding and van der Waals interactions are computed. In this analysis, a vast majority of thermophilic proteins adopt slightly lower free energy contribution in each energy terms than its mesophilic counterparts. The major observation noted from this study is the lower hydrophobic free energy contribution due to carbon atoms and main-chain nitrogen atoms in all the thermophilic proteins. The possible combination of different free energy terms shows majority of the thermophilic proteins have lower free energy strategy than their mesophilic homologous. The derived results show that the hydrophobic free energy due to carbon and nitrogen atoms and such combinations of free energy components play a vital role in the thermostablisation of such proteins.International Journal of Biological Macromolecules 05/2005; 35(3-4):211-20. · 2.45 Impact Factor -
Article: Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes.
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ABSTRACT: Understanding the factors influencing the stability of protein mutants is an important task in molecular and computational biology. In this work, we have approached this problem by examining the relative importance of secondary structure and solvent accessibility of the mutant residue for understanding/predicting the stability of protein mutants. We have used hydrophobic, electrostatic and hydrogen bond free energy terms and nine unique physicochemical, energetic and conformational properties of amino acids in the present study and these parameters have been related with changes in thermal stability (DeltaTm) of all the single mutants of lysozymes based on single and multiple correlation coefficients. As expected the properties reflecting hydrophobicity and hydrophobic free energy play a major role to distinguish stabilizing and destabilizing mutants. The hydrophobic free energy due to carbon and nitrogen atoms distinguish the stability of coil and strand mutations to the accuracy of 100 and 90%, respectively. In agreement with previous results, the subgroup classification based on secondary structure and the information about its location in the structure yielded good relationship with the experimental DeltaTm. We revealed that the secondary structure information is equally or more important than solvent accessibility for understanding the stability of protein mutants. The comparison of amino acid properties with free-energy terms indicate that the energetic contribution explains the mutant stability better in coil region whereas the amino acid properties do better in strand region. Further, the combination of free energies with amino acid properties increased the correlation significantly. The present study demonstrates the importance of classifying the mutants based on secondary structure to the stability of proteins upon mutations.Computational Biology and Chemistry 03/2005; 29(1):25-35. · 1.55 Impact Factor -
Article: Crystal Structure of an Azabicyclic Thiosemicarbazone Derivative
Molecular Crystals and Liquid Crystals. 01/2005; 442(1):31-39. -
Article: Crystal structure of 2,6‐diphenyl azabicyclo [3.3.1] nonan‐9‐one thiosemicarbazone
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ABSTRACT: The title compound (C21H24N4S, CCDC 206345) crystallizes in triclinic space group P&1macr; with cell parameters a =12.557(2) Å, b = 12.743(2) Å, c = 13.703(2) Å, =90.005(3)°, β = 113.663(3)°, = 106.756(3)°, V = 1906.2(5) Å3, Z = 4, Dcal = 1.270 Mg/m3 at T =293 K. The structure was solved by direct methods and refined by full-matrix least-squares procedures to a final R1= 0.0573and wR2 = 0.1364 using 8192 observed reflections. The piperidine and cyclohexane rings adopt chair conformation. The planar phenyl rings are the equatorial substituents of the piperidine ring. The molecules in the unit cell are stabilized by N-H…N, N-H…S & C-H…π intra and intermolecular hydrogen bond networks in addition to van der Waals forces. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)Crystal Research and Technology 08/2004; 39(9):821 - 826. · 0.95 Impact Factor -
Article: A study of aromatic hydrogen bonds of peptides with aromatic amino acid side-chains.
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ABSTRACT: The importance of hydrogen bonding studies lies in their structural, biological and medicinal applications. Non-conventional hydrogen bonds are weak, but are found to play an important role in biological molecules. In view of their importance,a study of the aromatic hydrogen bonds in peptides with aromatic amino acid side chains was carried out. The results indicate a reasonable probability for their occurrence, thereby enumerating their distinct features.Indian journal of biochemistry & biophysics 08/2004; 41(4):184-7. · 1.14 Impact Factor -
Article: Role of non-covalent interactions for determining the folding rate of two-state proteins.
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ABSTRACT: Understanding the factors influencing the folding rate of proteins is a challenging problem. In this work, we have analyzed the role of non-covalent interactions for the folding rate of two-state proteins by free-energy approach. We have computed the free-energy terms, hydrophobic, electrostatic, hydrogen-bonding and van der Waals free energies. The hydrophobic free energy has been divided into the contributions from different atoms, carbon, neutral nitrogen and oxygen, charged nitrogen and oxygen, and sulfur. All the free-energy terms have been related with the folding rates of 28 two-state proteins with single and multiple correlation coefficients. We found that the hydrophobic free energy due to carbon atoms and hydrogen-bonding free energy play important roles to determine the folding rate in combination with other free energies. The normalized energies with total number of residues showed better results than the total energy of the protein. The comparison of amino acid properties with free-energy terms indicates that the energetic terms explain better the folding rate than amino acid properties. Further, the combination of free energies with topological parameters yielded the correlation of 0.91. The present study demonstrates the importance of topology for determining the folding rate of two-state proteins.Biophysical Chemistry 03/2004; 107(3):263-72. · 2.20 Impact Factor -
Article: Structure and conformation of a nickel complex: {2‐Hydroxo‐3‐piperidine‐1‐yl‐methyl‐N,N′(bis‐5‐bromobenzylpropylenediimine)nickel(II)perchlorate}
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ABSTRACT: The title compound, a nickel complex [C23H26N3O2Br2Ni.(ClO4)] (CCDC 199520) crystallizes in triclinic space group P with the cell parameters a = 10.2560(4), b = 10.8231(4), c = 12.0888(5)Å, α = 99.404(1), β = 99.780(1), γ = 92.252(1)° and V = 1301.49(9)Å3. The structure was solved by Patterson method and refined by full-matrix least-squares procedures to a final R = 0.0497 using 6287 observed reflections. In the complex, the piperidine ring takes chair conformation and the geometry around the Ni ion is slightly distorted square planar. The dihedral angle between the planes [N-Ni-N and O-Ni-O] is 9.4(1)°. The chelate ring containing both the nitrogen atoms adopts twisted boat conformation. The molecules in the crystal are stabilized by N-H…O and C-H…O types of hydrogen bonds in addition to a C-H…π interaction. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)Crystal Research and Technology 02/2004; 39(2):185 - 192. · 0.95 Impact Factor -
Article: Purification and crystallization of haemoglobin from donkey (Equus asinus).
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ABSTRACT: Haemoglobin acts as an important protein for oxygen carrier in all living beings. Purification of donkey haemoglobin was done using PEG 4000 as a separating medium. Crystallization was achieved using hanging drop vapor diffusion method using 2.8 M phosphate buffer, pH 6.8. Data collection was done using mar345 image plate detector system. The crystals grown under 2.8 M phosphate buffer are monoclinic with space group C2 and cell dimensions a=107.664 A, b=63.084 A, c=54.042 A, and beta=111.747 degrees.Biochemical and Biophysical Research Communications 02/2004; 313(3):466-7. · 2.48 Impact Factor -
Article: A comparative study on structure and conformation of three hydroxybenzylamine ligands
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ABSTRACT: Structure and conformation of three tridentate ligands are determined. All these three compounds crystallize in different space groups, the details are as follows: Bis[(3,5-dimethyl,2-hydroxy)-2P[`1]P\bar 1 (a = 5.228(1), b = 12.364(1) , c = 13.234(1) , = 94.04(1), = 95.72(1), = 95.90(1)). The cyclohexane rings in DHBC and DHBrBC assume chair conformation. Both the phenyl rings are planar in all the molecules and orient at angles of 75.5(1), 62.2(1), and 53.9(2), respectively with each other. The bond angles around N atom show the sp3 character. Inter- and intramolecular O–HN and O–HO types of hydrogen bondings stabilize the molecules in the unit cell in addition to van der Waals forces.Journal of Chemical Crystallography 11/2003; 33(12):925-932. · 0.57 Impact Factor -
Article: t-3-Isopropyl-1-methyl-r-2,c-6-diphenylpiperidin-4-one thiosemicarbazone.
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ABSTRACT: The piperidine ring in the title compound, C(22)H(28)N(4)S, exhibits a chair conformation. The thiosemicarbazone moiety adopts an extended conformation, and the planar phenyl rings are oriented equatorially with respect to the piperidine ring. Two intermolecular hydrogen bonds involving the S atom form molecular pairs, and the crystal structure is stabilized by weak C-H.pi interactions in addition to van der Waals forces.Acta Crystallographica Section C Crystal Structure Communications 07/2003; 59(Pt 6):o346-8. · 0.52 Impact Factor -
Article: ROLE OF WEAK INTERACTIONS IN THE STRUCTURE OF 3-(α,α′-DIBROMOMETHYL)BENZYL 1-4 BENZOTRIAZOLE (DBT)
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ABSTRACT: 3-(α,α′-Dibromomethyl)benzyl 1-4 benzotriazole, C14H11Br2N3, F.W.=381.08, triclinic, P1¯ a=8.411(1)Å, b=9.008(1)Å, c=9.714(1)Å, α=97.74(1)°, β=103.11(1)°, γ=101.62(1)°,V=689.4(1)Å3, Z=2, Dcal=1.836 Mgm−3, μ=7.364 mm−1, λ(CuKα)=1.5418 Å, final R1 and wR2 are 0.0538 and 0.1383, respectively. The title compound is a precursor for the macroligand stilbenobenzotriazolophane. Unusual short bond length in the benzotriazole ring suggests the delocalization effect on the bonding. Intermolecular C–H…π, C–H…Br, and some face-to-face π-π interactions play a role in stabilizing the delocalized form. The molecules in the unit cell are stabilized by C–H…N type of interactions in addition to van der Waals forces.Molecular Crystals and Liquid Crystals 01/2003; 403(1):15-22. · 0.58 Impact Factor -
Article: Crystal structure of μ‐phenoxo bridged dicopper complex: {N‐[(2‐hydroxylato‐5‐methyl)benzyl‐(2′‐hydroxylato‐3′,5′‐dimethylbenzyl)]ethyl amine dicopper(II)}
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ABSTRACT: The title compound crystallizes in monoclinic space group C2/c with cell parameters a = 21.404(2), b = 13.962(1), c = 17.917(1)Å, β = 124.394(2)°, V = 4418.3(6)Å3, Z = 8, Dcal = 1.193Mg/m3 and T = 293 K. The structure was solved by Patterson method and refined by full-matrix least-squares procedures to final R = 0.0882 using 5253 observed reflections. The tetra coordinated copper atom have a slight distorted square planar geometry with the Cu-Cu distance of 2.987(1)Å. The two six membered rings containing copper atom assume distorted sofa conformation. C-H…π and C-H…O type of intermolecular interactions play a role in stabilizing the crystal packing in addition to van der Waals forces.Crystal Research and Technology 12/2002; 37(12):1360 - 1367. · 0.95 Impact Factor -
Article: Purification and crystallization of coconut globulin cocosin from Cocos nucifera.
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ABSTRACT: Cocosin is a legume class reserve protein found in coconut endosperm. Using coconut endosperm, two methods of purification were done. Crystallization was achieved by vapor diffusion (hanging drop) method using MPD, PEG 3350 and PEG 4000 as precipitants. X-ray diffraction data to 3.5-A resolution were collected using Mar345 image plate detector system. Crystals of cocosin grown under 20% MPD, are rhombohedral with space group R3 and cell dimensions a=92.829 A, b=92.829 A, c=215.290 A.Biochimica et Biophysica Acta 12/2002; 1601(1):121-2. · 4.66 Impact Factor -
Article: 9,9-Dimethoxy-7,11-diphenyl-2,4-diazaspiro[5.5]undecane-1,3,5-trione monohydrate.
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ABSTRACT: Due to steric repulsions, the cyclohexane ring in the title compound, C(23)H(24)N(2)O(5).H(2)O, shows some bond-length abnormalities and adopts a chair conformation. The pyrimidine and cyclohexane rings are approximately perpendicular to each other, and the phenyl rings are equatorial. C-H.pi and N-H.O intermolecular interactions, as well as C-H.O inter- and intramolecular interactions, occur between the molecules. In addition to van der Waals interactions, the water molecule interacts with the pyrimidinetrione ring to stabilize the structure.Acta Crystallographica Section C Crystal Structure Communications 12/2002; 58(Pt 11):o678-80. · 0.52 Impact Factor -
Article: 4-[3-(3,4-dimethoxyphenyl)prop-2-enoyl]phenyl methacrylate and 4-[3-(2-bromophenyl)prop-2-enoyl]phenyl methacrylate.
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ABSTRACT: Chalcones (alpha,beta-unsaturated ketones) are effective antitumour agents. It has been proved that having halogen or methoxy groups substituted in various positions of the phenyl ring enhances the activity of chalcones many times. The title compounds, C21H20O5 and C19H15BrO3, respectively, were chosen for crystallographic study in order to determine their structures and conformations. In both compounds, the keto group is in the s-cis conformation and is almost planar. There are weak intramolecular interactions in both structures.Acta Crystallographica Section C Crystal Structure Communications 02/2002; 58(Pt 1):o26-8. · 0.52 Impact Factor -
Article: Distribution of amino acid residues and residue-residue contacts in molecular chaperones.
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ABSTRACT: The amino acid distribution and residue-residue contacts in molecular chaperones are different when compared to normal globular proteins. The study of molecular chaperones reveals a different surrounding environment to exist for the residues Cys, Trp, and His which may play an important role in determining the chaperone structures. Unlike globular proteins, it has been observed that a one-to-one correspondence between the amino acid distribution in a sequence and the structures of molecular chaperones. The preference of amino acid residues surrounding all 20 types of residues in secondary structures and their accessible surface areas have been analysed.Preparative Biochemistry & Biotechnology 06/2001; 31(2):163-83. · 0.47 Impact Factor -
Article: Structural class prediction: an application of residue distribution along the sequence.
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ABSTRACT: Deciphering the native conformation of proteins from their amino acid sequences is one of the most challenging problems in molecular biology. Information on the secondary structure of a protein can be helpful in understanding its native folded state. In our earlier work on molecular chaperones, we have analyzed the hydrophobic and charged patches, short-, medium- and long-range contacts and residue distributions along the sequence. In this article, we have made an attempt to predict the structural class of globular and chaperone proteins based on the information obtained from residue distributions. This method predicts the structural class with an accuracy of 93 and 96%, respectively, for the four- and three-state models in a training set of 120 globular proteins, and 90 and 96%, respectively, for a test set of 80 proteins. We have used this information and methodology to predict the structural classes of chaperones. Interestingly most of the chaperone proteins are predicted under alpha/beta or mixed folding type.Biophysical Chemistry 01/2001; 88(1-3):81-101. · 2.20 Impact Factor -
Article: 6,7-Dihydrodibenzo[e,g]azulen-8(5H)-one and 12,13-dihydrobenzo[e]napth[2,1-g]azulen-14(11H)-one.
Acta Crystallographica Section C Crystal Structure Communications 08/2000; 56 ( Pt 7):824-6. · 0.52 Impact Factor
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Institutions
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1998–2013
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University of Madras
- Department of Crystallography and Biophysics
Chennai, State of Tamil Nadu, India
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