U. Chandra Singh

Bio: U. Chandra Singh is an academic researcher from University of California, San Francisco. The author has contributed to research in topics: Free energy perturbation & Molecular dynamics. The author has an hindex of 7, co-authored 8 publications receiving 3993 citations. Previous affiliations of U. Chandra Singh include Scripps Health.

An approach to computing electrostatic charges for molecules

Abstract: We present an approach for deriving net atomic charges from ab initio quantum mechanical calculations using a least squares fit of the quantum mechanically calculated electrostatic potential to that of the partial charge model. Our computational approach is similar to those presented by Momany [J. Phys. Chem., 82, 592 (1978)], Smit, Derissen, and van Duijneveldt [Mol. Phys., 37, 521 (1979)], and Cox and Williams [J. Comput. Chem., 2, 304 (1981)], but differs in the approach to choosing the positions for evaluating the potential. In this article, we present applications to the molecules H2O, CH3OH, (CH3)2O, H2CO, NH3, (CH3O)2PO, deoxyribose, ribose, adenine, 9-CH3 adenine, thymine, 1-CH3 thymine, guanine, 9-CH3 guanine, cytosine, 1-CH3 cytosine, uracil, and 1-CH3 uracil. We also address the question of inclusion of “lone pairs,” their location and charge.

A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers

Abstract: We present an approach to couple ab initio quantum mechanical geometry optimiuzations with molecular mechanical optimizations, with the added capability to carry out molecular dynamics simulations of the systems to earch for new local minima. The approach is applied to the aqueous solution CH3Cl + Cl− exchange reaction and the gas phase protonation of polyethers.

Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin

Abstract: Site-directed mutagenesis is a very powerful approach to altering the biological functions of proteins, the structural stability of proteins and the interactions of proteins with other molecules. Several experimental studies in recent years have been directed at estimating the changes in catalytic properties, (rates of binding and catalysis) in site-directed mutants of enzymes compared to the native enzymes. Simulation approaches to the study of complex molecules have also become more powerful, in no small measure owing to the increase in computer power. These simulations have often allowed results of experiments to be rationalized and understood mechanistically. A new approach called the free-energy pertubation method, which uses statistical mechanics and molecular dynamics can often be used for quantitative calculation of free energy differences. We have applied such a technique to calculate the differential free energy of binding and free energy of activation for catalysis of a tripeptide substrate by native subtilisin and a subtilisin mutant (Asn 155----Ala 155). Our studies lead to a calculated difference in free energy of binding which is relatively small, but a calculated change in free energy of catalysis which is substantial. These energies are very close to those determined experimentally (J. A. Wells and D. A. Estell, personal communication), which were not known to us until the simulations were completed. This demonstrates the predictive power and utility of theoretical simulation methods in studies of the effects of site-specific mutagenesis on both enzyme binding and catalysis.

Molecular Dynamics Simulations of DNA Double Helices: Studies of Sequence Dependence and the Role of Mismatch Pairs in the DNA Helix

Abstract: We present the results of molecular dynamics simulations on base paired deoxyribonucleotides dA10·dT10, d(GCGCGCGCGC)2 d(ATATATATAT)2 d(CGCGA)·d(TCACG) (AC mismatch) and d(CGAGA)·d(TCGCG) (GA mismatch). The average structural properties — helix parameters, H-bond parameters, sugar puckers, torsional angles, root mean square atomic fluctuations — are compared to those found in earlier studies on the sequence d(CGCGA)·d(TCGCG).1 The properties of the decamer helices remain B DNA like throughout the simulation, confirming our inference1 that a model which treats solvent/counterions in a simple fashion (full charge on phosphates, but use of large hydrated counterions and a distance dependent dielectric constant) is a reasonable “first order” model to simulate the properties of DNA helices over periods of at least 100 psec. There are a number of sequence dependent effects observed in the three decanucleotides studied here, among them differences in H-bond properties, sugar pucker and helix repeat/base tilts. In d(GCGCGCGCGC)2 and d(ATATATATAT)2 the H-bonds all stay near the classic Watson-Crick distance and the base tilts and twists are small (10–20°). On the other hand, in dA10·dT10 there are much larger deviations of H-bonding from classic Watson-Crick and H-bond exchange during the simulation. There are many more examples of sugar repuckering in the AT decamers, and the relative frequency of such repuckering is qualitatively consistent with what one would expect based on molecular mechanics studies. A comparison of the torsional angles, sugar puckers, helical parameters, root mean square atom amplitudes and hydrogen bond parameters of the sequence d(CGCGA)·d(TCGCG) with the two mismatched analogues demonstrates that the effect of the poorer hydrogen bonding at the central base pair is transmitted throughout the sequence, leading to significantly greater root mean square fluctuations in all dihedral angles, significantly higher % of non-“standard C2′ endo” sugar puckers, generally longer H-bond distances, with greater % of “long” H bonds during the simulation, larger RMS amplitude of atomic fluctuations and greater helix twist and tilt of the base pairs. The average helix repeat is 9.0 for the AC mismatch, and 10.1 for the GA mismatch, compared to 10.0 for the normal sequence.

Modeling complex molecular interactions involving proteins and DNA.

Abstract: We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum mechanics in studies of enzyme substrate interactions. It is our perspective that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules. In the area of DNA molecular mechanics and dynamics, it is clear that the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics. Finally, we are in a position to reasonably simulate structures and (qualitatively) energies for complete reaction pathways of enzymes using a combination of computer graphics, molecular mechanics and quantum mechanics. More accurate energies and pathways are sure to follow, using the combined molecular mechanics/quantum mechanics optimization developed by Singh and the free energy perturbation methods pioneered in Groningen and Houston.

Chemistry with ADF

Abstract: We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001

The Amber biomolecular simulation programs

Abstract: We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

CHARMM: the biomolecular simulation program.

Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Abstract: The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.

An all atom force field for simulations of proteins and nucleic acids.

Abstract: We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.